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Created September 12, 2014 09:25
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prof_mri.txt
Thread ID: 70106778563460
Fiber ID: 70106803971780
Total Time: 1395.160051023
Sort by: total_time
%total %self total self wait child calls Name
--------------------------------------------------------------------------------
100.00% 0.00% 1395.160 0.000 0.000 1395.160 1 Global#[No method]
1395.159 0.000 0.000 1395.158 1/1 BioPieces::Pipeline#run
0.001 0.000 0.000 0.001 1/1 BioPieces::Commands#plot_scores
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#read_fastq
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#grab
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#trim_seq
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#mean_scores
0.000 0.000 0.000 0.000 1/371171 Class#new
--------------------------------------------------------------------------------
1395.159 0.000 0.000 1395.158 1/1 Global#[No method]
100.00% 0.00% 1395.159 0.000 0.000 1395.158 1 BioPieces::Pipeline#run
1395.157 0.000 0.000 1395.157 1/1 BioPieces::Pipeline#run_thread
0.001 0.000 0.000 0.001 1/1 BioPieces::StatusHelper#status_init
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed_values
0.000 0.000 0.000 0.000 1/3 BioPieces::OptionsHelper#options_tie
0.000 0.000 0.000 0.000 1/3 BioPieces::OptionsHelper#options_conflict
--------------------------------------------------------------------------------
1395.157 0.000 0.000 1395.157 1/1 BioPieces::Pipeline#run
100.00% 0.00% 1395.157 0.000 0.000 1395.157 1 BioPieces::Pipeline#run_thread
1395.123 0.000 0.000 1395.122 1/1 BioPieces::Pipeline::Command#run
0.034 0.001 0.000 0.034 1/278 Array#each
0.000 0.000 0.000 0.000 1/33 Array#first
0.000 0.000 0.000 0.000 1/1 Array#[]
0.000 0.000 0.000 0.000 1/2 Array#reverse
--------------------------------------------------------------------------------
1395.123 0.000 0.000 1395.122 1/1 BioPieces::Pipeline#run_thread
100.00% 0.00% 1395.123 0.000 0.000 1395.122 1 BioPieces::Pipeline::Command#run
1395.122 0.000 0.000 1395.122 1/131 Proc#call
0.000 0.000 0.000 0.000 1/8 <Class::Time>#now
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 5/131 Array#each
0.000 0.000 0.000 0.000 1/131 BioPieces::StatusHelper#status_track
0.000 0.000 0.000 0.000 60/131 Hash#each_pair
0.000 0.000 0.000 0.000 47/131 PrettyPrint#breakable
0.000 0.000 0.000 0.000 17/131 PrettyPrint::Breakable#output
1395.122 0.000 0.000 1395.122 1/131 BioPieces::Pipeline::Command#run
100.00% 0.00% 1395.122 0.000 0.000 1395.122 131 *Proc#call
1394.851 0.000 0.000 1394.851 1/1 BioPieces::StatusHelper#status_track
1394.414 0.000 0.000 1394.414 1/1 Kernel#catch
0.262 0.000 0.000 0.261 1/1 BioPieces::LogHelper#log_ok
0.084 0.000 0.000 0.083 1/2 BioPieces::StatusHelper#status_save
0.028 0.002 0.000 0.026 65/65 PP::PPMethods#comma_breakable
0.007 0.000 0.000 0.007 1/1 BioPieces::StatusHelper#status_load
0.003 0.000 0.000 0.002 1/1 BioPieces::HistoryHelper#history_save
0.001 0.001 0.000 0.000 64/64 String#*
0.000 0.000 0.000 0.000 1/278 Array#each
--------------------------------------------------------------------------------
1394.851 0.000 0.000 1394.851 1/1 Proc#call
99.98% 0.00% 1394.851 0.000 0.000 1394.851 1 BioPieces::StatusHelper#status_track
0.328 0.001 0.000 0.327 1/278 Array#each
0.026 0.000 0.000 0.026 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/8 <Class::Time>#now
0.000 0.000 0.000 0.000 1/2 Array#reverse
0.000 0.000 0.000 0.000 1/131 Proc#call
--------------------------------------------------------------------------------
1394.414 0.000 0.000 1394.414 1/1 Proc#call
99.95% 0.00% 1394.414 0.000 0.000 1394.414 1 Kernel#catch
1394.414 37.705 16.384 1340.324 1/1 Range#each
--------------------------------------------------------------------------------
1394.414 37.705 16.384 1340.324 1/1 Kernel#catch
99.95% 2.70% 1394.414 37.705 16.384 1340.324 1 Range#each
905.148 31.047 0.000 874.101 370638/370638 BioPieces::Stream#write
294.170 40.857 0.000 253.313 370639/370639 BioPieces::Fastq#get_entry
45.027 12.169 3.581 29.277 370638/370638 BioPieces::Seq#qual_valid?
36.953 19.456 7.003 10.494 370638/370638 BioPieces::Seq#qual_convert!
27.601 14.485 5.423 7.693 370638/370638 BioPieces::Seq#qual_coerce!
16.701 16.701 0.000 0.000 370638/370638 BioPieces::Seq#to_bp
13.441 8.024 3.283 2.134 370638/370638 BioPieces::Seq#length
1.219 1.219 0.000 0.000 185319/2038581 Symbol#==
0.064 0.000 0.000 0.063 2/2 <Class::BioPieces::Filesys>#open
0.000 0.000 0.000 0.000 1/1 BioPieces::Seq#qual_base33?
--------------------------------------------------------------------------------
905.148 31.047 0.000 874.101 370638/370638 Range#each
64.88% 2.23% 905.148 31.047 0.000 874.101 370638 BioPieces::Stream#write
839.549 24.061 815.487 0.000 741276/741285 IO#write
30.547 15.957 5.819 8.771 370638/370638 <Module::MessagePack>#pack
4.006 4.006 0.000 0.000 370638/370638 Array#pack
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/741285 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 7/741285 IO#puts
839.549 24.061 815.487 0.000 741276/741285 BioPieces::Stream#write
60.18% 1.72% 839.549 24.062 815.487 0.000 741285 IO#write
--------------------------------------------------------------------------------
294.170 40.857 0.000 253.313 370639/370639 Range#each
21.09% 2.93% 294.170 40.857 0.000 253.313 370639 BioPieces::Fastq#get_entry
209.560 15.592 193.967 0.000 1482553/1482553 IO#gets
33.678 5.622 0.351 27.705 370638/371171 Class#new
6.971 6.971 0.000 0.000 1111914/1111914 String#chomp!
3.079 3.079 0.000 0.000 370638/370638 String#[]
0.025 0.000 0.000 0.025 2/2 BioPieces::Filesys#close
0.000 0.000 0.000 0.000 1/3 BasicObject#method_missing
--------------------------------------------------------------------------------
209.560 15.592 193.967 0.000 1482553/1482553 BioPieces::Fastq#get_entry
15.02% 1.12% 209.560 15.592 193.967 0.000 1482553 IO#gets
--------------------------------------------------------------------------------
45.027 12.169 3.581 29.277 370638/370638 Range#each
3.23% 0.87% 45.027 12.169 3.581 29.277 370638 BioPieces::Seq#qual_valid?
27.202 4.808 1.120 21.274 370638/370639 String#match
2.076 2.076 0.000 0.000 370638/1111914 Kernel#nil?
--------------------------------------------------------------------------------
36.953 19.456 7.003 10.494 370638/370638 Range#each
2.65% 1.39% 36.953 19.456 7.003 10.494 370638 BioPieces::Seq#qual_convert!
10.494 10.494 0.000 0.000 1853190/2038581 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/371171 Tempfile#initialize
0.000 0.000 0.000 0.000 2/371171 PrettyPrint#initialize
0.000 0.000 0.000 0.000 1/371171 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/371171 BioPieces::Commands#mean_scores
0.000 0.000 0.000 0.000 1/371171 BioPieces::Commands#grab
0.000 0.000 0.000 0.000 1/371171 BioPieces::Commands#plot_scores
0.000 0.000 0.000 0.000 1/371171 BioPieces::Commands#trim_seq
0.000 0.000 0.000 0.000 1/371171 BioPieces::Commands#read_fastq
0.000 0.000 0.000 0.000 1/371171 Global#[No method]
0.000 0.000 0.000 0.000 10/371171 <Class::BioPieces::Stream>#pipe
0.000 0.000 0.000 0.000 2/371171 <Class::BioPieces::Filesys>#open
0.001 0.000 0.000 0.001 1/371171 <Class::PP>#pp
0.001 0.000 0.000 0.001 6/371171 Array#map
0.003 0.001 0.000 0.001 91/371171 PrettyPrint#text
0.008 0.001 0.000 0.007 91/371171 PrettyPrint#breakable
0.010 0.004 0.000 0.006 317/371171 PrettyPrint#group_sub
33.678 5.622 0.351 27.705 370638/371171 BioPieces::Fastq#get_entry
2.42% 0.40% 33.702 5.630 0.351 27.721 371171 *Class#new
27.705 13.556 14.149 0.000 370638/370638 BioPieces::Seq#initialize
0.007 0.005 0.000 0.002 91/91 PrettyPrint::Breakable#initialize
0.006 0.006 0.000 0.000 318/318 PrettyPrint::Group#initialize
0.001 0.000 0.000 0.001 6/6 Tempfile#initialize
0.001 0.001 0.000 0.000 91/91 PrettyPrint::Text#initialize
0.001 0.000 0.000 0.000 1/1 PrettyPrint#initialize
0.000 0.000 0.000 0.000 1/1 PrettyPrint::GroupQueue#initialize
0.000 0.000 0.000 0.000 2/2 BioPieces::Filesys#initialize
0.000 0.000 0.000 0.000 10/10 BioPieces::Stream#initialize
0.000 0.000 0.000 0.000 6/6 BioPieces::Pipeline::Command#initialize
0.000 0.000 0.000 0.000 6/6 Tempfile::Remover#initialize
0.000 0.000 0.000 0.000 1/1 BioPieces::Pipeline#initialize
--------------------------------------------------------------------------------
30.547 15.957 5.819 8.771 370638/370638 BioPieces::Stream#write
2.19% 1.14% 30.547 15.957 5.819 8.771 370638 <Module::MessagePack>#pack
8.771 8.771 0.000 0.000 1482552/1482651 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
27.705 13.556 14.149 0.000 370638/370638 Class#new
1.99% 0.97% 27.705 13.556 14.149 0.000 370638 BioPieces::Seq#initialize
--------------------------------------------------------------------------------
27.601 14.485 5.423 7.693 370638/370638 Range#each
1.98% 1.04% 27.601 14.485 5.423 7.693 370638 BioPieces::Seq#qual_coerce!
5.546 5.546 0.000 0.000 370638/370638 String#tr!
2.148 2.148 0.000 0.000 370638/1111914 Kernel#nil?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/370639 BioPieces::Seq#qual_base33?
27.202 4.808 1.120 21.274 370638/370639 BioPieces::Seq#qual_valid?
1.95% 0.34% 27.202 4.808 1.120 21.274 370639 String#match
21.274 17.237 4.037 0.000 370639/370639 Regexp#match
--------------------------------------------------------------------------------
21.274 17.237 4.037 0.000 370639/370639 String#match
1.52% 1.24% 21.274 17.237 4.037 0.000 370639 Regexp#match
--------------------------------------------------------------------------------
16.701 16.701 0.000 0.000 370638/370638 Range#each
1.20% 1.20% 16.701 16.701 0.000 0.000 370638 BioPieces::Seq#to_bp
--------------------------------------------------------------------------------
13.441 8.024 3.283 2.134 370638/370638 Range#each
0.96% 0.58% 13.441 8.024 3.283 2.134 370638 BioPieces::Seq#length
2.134 2.134 0.000 0.000 370638/1111914 Kernel#nil?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 22/2038581 Array#include?
0.000 0.000 0.000 0.000 50/2038581 Hash#each
1.219 1.219 0.000 0.000 185319/2038581 Range#each
10.494 10.494 0.000 0.000 1853190/2038581 BioPieces::Seq#qual_convert!
0.84% 0.84% 11.713 11.713 0.000 0.000 2038581 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/1482651 Kernel#rand
0.000 0.000 0.000 0.000 2/1482651 Hash#==
0.000 0.000 0.000 0.000 9/1482651 Kernel#respond_to?
0.001 0.001 0.000 0.000 82/1482651 <Module::Marshal>#dump
8.771 8.771 0.000 0.000 1482552/1482651 <Module::MessagePack>#pack
0.63% 0.63% 8.772 8.772 0.000 0.000 1482651 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
6.971 6.971 0.000 0.000 1111914/1111914 BioPieces::Fastq#get_entry
0.50% 0.50% 6.971 6.971 0.000 0.000 1111914 String#chomp!
--------------------------------------------------------------------------------
2.076 2.076 0.000 0.000 370638/1111914 BioPieces::Seq#qual_valid?
2.134 2.134 0.000 0.000 370638/1111914 BioPieces::Seq#length
2.148 2.148 0.000 0.000 370638/1111914 BioPieces::Seq#qual_coerce!
0.46% 0.46% 6.357 6.357 0.000 0.000 1111914 Kernel#nil?
--------------------------------------------------------------------------------
5.546 5.546 0.000 0.000 370638/370638 BioPieces::Seq#qual_coerce!
0.40% 0.40% 5.546 5.546 0.000 0.000 370638 String#tr!
--------------------------------------------------------------------------------
4.006 4.006 0.000 0.000 370638/370638 BioPieces::Stream#write
0.29% 0.29% 4.006 4.006 0.000 0.000 370638 Array#pack
--------------------------------------------------------------------------------
3.079 3.079 0.000 0.000 370638/370638 BioPieces::Fastq#get_entry
0.22% 0.22% 3.079 3.079 0.000 0.000 370638 String#[]
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 11/278 PrettyPrint::GroupQueue#deq
0.000 0.000 0.000 0.000 91/278 PrettyPrint::Text#output
0.000 0.000 0.000 0.000 102/278 Array#each
0.000 0.000 0.000 0.000 1/278 BioPieces::OptionsHelper#options_required
0.000 0.000 0.000 0.000 1/278 Proc#call
0.000 0.000 0.000 0.000 1/278 BioPieces::OptionsHelper#options_required_unique
0.000 0.000 0.000 0.000 3/278 BioPieces::OptionsHelper#options_unique
0.000 0.000 0.000 0.000 2/278 BioPieces::OptionsHelper#options_files_exists_force
0.000 0.000 0.000 0.000 2/278 BioPieces::OptionsHelper#options_files_exist
0.000 0.000 0.000 0.000 1/278 BioPieces::OptionsHelper#options_glob
0.000 0.000 0.000 0.000 1/278 PrettyPrint::GroupQueue#initialize
0.000 0.000 0.000 0.000 6/278 <Class::Dir>#tmpdir
0.000 0.000 0.000 0.000 48/278 PrettyPrint#flush
0.003 0.000 0.000 0.002 2/278 BioPieces::Pipeline#to_s
0.007 0.000 0.000 0.007 1/278 BioPieces::StatusHelper#status_load
0.034 0.001 0.000 0.034 1/278 BioPieces::Pipeline#run_thread
0.249 0.000 0.000 0.248 3/278 PP::PPMethods#seplist
0.328 0.001 0.000 0.327 1/278 BioPieces::StatusHelper#status_track
0.04% 0.00% 0.621 0.002 0.000 0.619 278 *Array#each
0.327 0.000 0.327 0.000 5/5 Thread#join
0.033 0.030 0.003 0.000 5/5 <Class::Thread>#new
0.005 0.003 0.000 0.002 6/6 <Module::Marshal>#load
0.005 0.003 0.000 0.002 53/91 PrettyPrint::Breakable#output
0.003 0.001 0.000 0.002 53/91 PrettyPrint::Text#output
0.002 0.001 0.000 0.002 12/12 BioPieces::Pipeline::Command#to_s
0.002 0.001 0.000 0.000 107/107 Integer#downto
0.001 0.001 0.000 0.000 6/12 <Class::IO>#read
0.001 0.000 0.000 0.000 5/5 <Class::BioPieces::Stream>#pipe
0.001 0.001 0.000 0.000 96/144 Array#clear
0.000 0.000 0.000 0.000 16/27 PrettyPrint::Group#break
0.000 0.000 0.000 0.000 1/318 PrettyPrint::GroupQueue#enq
0.000 0.000 0.000 0.000 6/6 <Class::File>#expand_path
0.000 0.000 0.000 0.000 6/6 <Class::File>#stat
0.000 0.000 0.000 0.000 4/4 <Class::File>#file?
0.000 0.000 0.000 0.000 2/2 String#split
0.000 0.000 0.000 0.000 6/6 File::Stat#writable?
0.000 0.000 0.000 0.000 1/1 Module#include
0.000 0.000 0.000 0.000 6/6 File::Stat#world_writable?
0.000 0.000 0.000 0.000 6/28 Kernel#is_a?
0.000 0.000 0.000 0.000 7/7 Module#method_added
0.000 0.000 0.000 0.000 6/6 File::Stat#directory?
0.000 0.000 0.000 0.000 6/6 File::Stat#sticky?
0.000 0.000 0.000 0.000 2/2 IO#set_encoding
0.000 0.000 0.000 0.000 2/2 String#include?
0.000 0.000 0.000 0.000 1/1 Class#inherited
0.000 0.000 0.000 0.000 1/1 BasicObject#singleton_method_added
0.000 0.000 0.000 0.000 102/278 Array#each
0.000 0.000 0.000 0.000 5/131 Proc#call
0.000 0.000 0.000 0.000 8/155 PP::PPMethods#pp
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/12 Dir::Tmpname#create
0.000 0.000 0.000 0.000 2/12 <Class::BioPieces::Filesys>#open
0.002 0.000 0.000 0.002 1/12 BioPieces::HistoryHelper#history_save
0.104 0.000 0.000 0.104 2/12 BioPieces::StatusHelper#status_save
0.261 0.000 0.000 0.261 1/12 BioPieces::LogHelper#log_ok
0.03% 0.00% 0.368 0.000 0.000 0.368 12 <Class::IO>#open
0.258 0.000 0.000 0.258 1/1 <Class::PP>#pp
0.105 0.002 0.000 0.104 12/14 File#initialize
0.004 0.000 0.000 0.003 4/4 IO#puts
0.001 0.001 0.000 0.000 2/7 IO#close
--------------------------------------------------------------------------------
0.327 0.000 0.327 0.000 5/5 Array#each
0.02% 0.00% 0.327 0.000 0.327 0.000 5 Thread#join
--------------------------------------------------------------------------------
0.262 0.000 0.000 0.261 1/1 Proc#call
0.02% 0.00% 0.262 0.000 0.000 0.261 1 BioPieces::LogHelper#log_ok
0.261 0.000 0.000 0.261 1/12 <Class::IO>#open
0.000 0.000 0.000 0.000 1/20 <Object::Object>#[]
--------------------------------------------------------------------------------
0.258 0.000 0.000 0.258 1/1 <Class::IO>#open
0.02% 0.00% 0.258 0.000 0.000 0.258 1 <Class::PP>#pp
0.257 0.000 0.000 0.257 1/1 PP::PPMethods#guard_inspect_key
0.001 0.000 0.000 0.001 1/371171 Class#new
0.000 0.000 0.000 0.000 1/48 PrettyPrint#flush
--------------------------------------------------------------------------------
0.257 0.000 0.000 0.257 1/1 <Class::PP>#pp
0.02% 0.00% 0.257 0.000 0.000 0.257 1 PP::PPMethods#guard_inspect_key
0.257 0.000 0.000 0.257 1/155 PP::PPMethods#pp
0.000 0.000 0.000 0.000 2/2 Hash#==
0.000 0.000 0.000 0.000 5/780 Thread#[]
0.000 0.000 0.000 0.000 5/780 <Class::Thread>#current
0.000 0.000 0.000 0.000 1/1 Kernel#taint
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 8/155 Array#each
0.000 0.000 0.000 0.000 146/155 PrettyPrint#nest
0.257 0.000 0.000 0.257 1/155 PP::PPMethods#guard_inspect_key
0.02% 0.00% 0.257 0.000 0.000 0.257 155 *PP::PPMethods#pp
0.256 0.000 0.000 0.256 155/317 PrettyPrint#group
0.013 0.007 0.000 0.006 155/155 PP::PPMethods#check_inspect_key
0.007 0.004 0.000 0.003 155/155 PP::PPMethods#pop_inspect_key
0.005 0.003 0.000 0.002 155/155 PP::PPMethods#push_inspect_key
0.001 0.001 0.000 0.000 155/155 Kernel#object_id
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/317 Array#pretty_print
0.000 0.000 0.000 0.000 13/317 PP::PPMethods#pp_hash
0.000 0.000 0.000 0.000 73/317 PrettyPrint#nest
0.000 0.000 0.000 0.000 73/317 Hash#each_pair
0.256 0.000 0.000 0.256 155/317 PP::PPMethods#pp
0.02% 0.00% 0.256 0.000 0.000 0.256 317 *PrettyPrint#group
0.256 0.000 0.000 0.256 317/317 PrettyPrint#group_sub
0.048 0.029 0.000 0.020 634/911 PrettyPrint#text
--------------------------------------------------------------------------------
0.256 0.000 0.000 0.256 317/317 PrettyPrint#group
0.02% 0.00% 0.256 0.000 0.000 0.256 317 *PrettyPrint#group_sub
0.256 0.000 0.000 0.255 317/317 PrettyPrint#nest
0.010 0.004 0.000 0.006 317/371171 Class#new
0.006 0.006 0.000 0.000 317/318 PrettyPrint::GroupQueue#enq
0.006 0.004 0.000 0.002 244/317 PrettyPrint::GroupQueue#delete
0.002 0.002 0.000 0.000 317/408 Array#push
0.002 0.002 0.000 0.000 317/1151 Array#last
0.002 0.002 0.000 0.000 317/317 Array#pop
--------------------------------------------------------------------------------
0.256 0.000 0.000 0.255 317/317 PrettyPrint#group_sub
0.02% 0.00% 0.256 0.000 0.000 0.255 317 *PrettyPrint#nest
0.255 0.000 0.000 0.255 13/13 Hash#pretty_print
0.255 0.000 0.000 0.254 16/16 PP::PPMethods#seplist
0.250 0.000 0.000 0.249 3/3 Array#pretty_print
0.040 0.007 0.000 0.033 109/109 PP::ObjectMixin#pretty_print
0.012 0.004 0.000 0.008 73/138 PrettyPrint#breakable
0.005 0.002 0.000 0.003 73/911 PrettyPrint#text
0.004 0.001 0.000 0.003 28/28 Numeric#pretty_print
0.000 0.000 0.000 0.000 2/2 TrueClass#pretty_print
0.000 0.000 0.000 0.000 146/155 PP::PPMethods#pp
0.000 0.000 0.000 0.000 73/317 PrettyPrint#group
--------------------------------------------------------------------------------
0.255 0.000 0.000 0.255 13/13 PrettyPrint#nest
0.02% 0.00% 0.255 0.000 0.000 0.255 13 *Hash#pretty_print
0.255 0.000 0.000 0.255 13/13 PP::PPMethods#pp_hash
--------------------------------------------------------------------------------
0.255 0.000 0.000 0.255 13/13 Hash#pretty_print
0.02% 0.00% 0.255 0.000 0.000 0.255 13 *PP::PPMethods#pp_hash
0.000 0.000 0.000 0.000 13/317 PrettyPrint#group
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/15 BioPieces::Pipeline#to_s
0.254 0.000 0.000 0.254 13/15 PP::PPMethods#seplist
0.02% 0.00% 0.255 0.000 0.000 0.254 15 *Hash#each_pair
0.000 0.000 0.000 0.000 4/48 Symbol#to_s
0.000 0.000 0.000 0.000 2/2 FalseClass#to_s
0.000 0.000 0.000 0.000 2/6 TrueClass#to_s
0.000 0.000 0.000 0.000 73/317 PrettyPrint#group
0.000 0.000 0.000 0.000 60/131 Proc#call
--------------------------------------------------------------------------------
0.255 0.000 0.000 0.254 16/16 PrettyPrint#nest
0.02% 0.00% 0.255 0.000 0.000 0.254 16 *PP::PPMethods#seplist
0.254 0.000 0.000 0.254 13/15 Hash#each_pair
0.249 0.000 0.000 0.248 3/278 Array#each
0.001 0.001 0.000 0.000 16/23 Kernel#lambda
--------------------------------------------------------------------------------
0.250 0.000 0.000 0.249 3/3 PrettyPrint#nest
0.02% 0.00% 0.250 0.000 0.000 0.249 3 *Array#pretty_print
0.000 0.000 0.000 0.000 3/317 PrettyPrint#group
--------------------------------------------------------------------------------
0.026 0.000 0.000 0.026 1/2 BioPieces::StatusHelper#status_track
0.084 0.000 0.000 0.083 1/2 Proc#call
0.01% 0.00% 0.110 0.000 0.000 0.109 2 BioPieces::StatusHelper#status_save
0.104 0.000 0.000 0.104 2/12 <Class::IO>#open
0.005 0.001 0.000 0.004 2/33 Hash#each
0.000 0.000 0.000 0.000 1/1 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/10 Kernel#respond_to?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/14 Delegator#method_missing
0.105 0.002 0.000 0.104 12/14 <Class::IO>#open
0.01% 0.00% 0.105 0.002 0.000 0.104 14 *File#initialize
0.088 0.001 0.084 0.003 2/2 Delegator#method_missing
0.014 0.000 0.014 0.000 2/7 IO#close
0.002 0.001 0.000 0.001 2/36 <Module::Marshal>#dump
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0.000 0.000 0.000 0.000 2/8 File#to_path
--------------------------------------------------------------------------------
0.088 0.001 0.084 0.003 2/2 File#initialize
0.01% 0.00% 0.088 0.001 0.084 0.003 2 Delegator#method_missing
0.002 0.000 0.000 0.002 2/3 BasicObject#method_missing
0.000 0.000 0.000 0.000 2/2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/10 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/12 #<Class:0x007f8605e90f88>#__getobj__
0.000 0.000 0.000 0.000 2/14 File#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/911 TrueClass#pretty_print
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0.005 0.002 0.000 0.003 73/911 PrettyPrint#nest
0.008 0.003 0.000 0.004 65/911 PP::PPMethods#comma_breakable
0.017 0.004 0.000 0.013 109/911 PP::ObjectMixin#pretty_print
0.048 0.029 0.000 0.020 634/911 PrettyPrint#group
0.01% 0.00% 0.081 0.040 0.000 0.041 911 PrettyPrint#text
0.022 0.008 0.000 0.014 605/696 PrettyPrint#break_outmost_groups
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--------------------------------------------------------------------------------
0.064 0.000 0.000 0.063 2/2 Range#each
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0.000 0.000 0.000 0.000 2/371171 Class#new
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--------------------------------------------------------------------------------
0.062 0.061 0.001 0.000 2/2 <Class::BioPieces::Filesys>#open
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--------------------------------------------------------------------------------
0.040 0.007 0.000 0.033 109/109 PrettyPrint#nest
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/7 BioPieces::Stream#close
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0.033 0.030 0.003 0.000 5/5 Array#each
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--------------------------------------------------------------------------------
0.012 0.004 0.000 0.008 73/138 PrettyPrint#nest
0.019 0.004 0.000 0.015 65/138 PP::PPMethods#comma_breakable
0.00% 0.00% 0.031 0.007 0.000 0.023 138 PrettyPrint#breakable
0.011 0.001 0.000 0.010 47/48 PrettyPrint#flush
0.008 0.001 0.000 0.007 91/371171 Class#new
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--------------------------------------------------------------------------------
0.028 0.002 0.000 0.026 65/65 Proc#call
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--------------------------------------------------------------------------------
0.025 0.000 0.000 0.025 2/2 BioPieces::Fastq#get_entry
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--------------------------------------------------------------------------------
0.001 0.001 0.000 0.000 91/696 PrettyPrint#breakable
0.022 0.008 0.000 0.014 605/696 PrettyPrint#text
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0.006 0.000 0.000 0.006 11/11 PrettyPrint::GroupQueue#deq
0.004 0.002 0.000 0.002 38/91 PrettyPrint::Breakable#output
0.003 0.001 0.000 0.002 38/91 PrettyPrint::Text#output
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--------------------------------------------------------------------------------
0.013 0.007 0.000 0.006 155/155 PP::PPMethods#pp
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0.000 0.000 0.000 0.000 1/48 <Class::PP>#pp
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--------------------------------------------------------------------------------
0.010 0.010 0.000 0.000 605/605 PrettyPrint#text
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--------------------------------------------------------------------------------
0.004 0.002 0.000 0.002 38/91 PrettyPrint#break_outmost_groups
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0.002 0.001 0.000 0.001 73/317 PrettyPrint::Breakable#output
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0.007 0.005 0.000 0.002 91/91 Class#new
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0.007 0.000 0.000 0.007 1/1 Proc#call
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0.000 0.000 0.000 0.000 91/1151 PrettyPrint#current_group
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0.00% 0.00% 0.007 0.007 0.000 0.000 1151 Array#last
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0.000 0.000 0.000 0.000 3/33 BioPieces::OptionsHelper#options_tie
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0.007 0.004 0.000 0.003 155/155 PP::PPMethods#pp
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0.006 0.000 0.000 0.006 11/11 PrettyPrint#break_outmost_groups
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0.006 0.006 0.000 0.000 318/318 Class#new
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0.005 0.003 0.000 0.002 6/6 Array#each
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0.005 0.003 0.000 0.002 155/155 PP::PPMethods#pp
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 5/780 PP::PPMethods#guard_inspect_key
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 5/780 PP::PPMethods#guard_inspect_key
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0.004 0.000 0.000 0.003 4/4 <Class::IO>#open
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0.000 0.000 0.000 0.000 6/632 Dir::Tmpname#make_tmpname
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0.004 0.001 0.000 0.003 28/28 PrettyPrint#nest
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0.003 0.002 0.000 0.001 28/911 PrettyPrint#text
0.000 0.000 0.000 0.000 25/25 Fixnum#inspect
0.000 0.000 0.000 0.000 3/3 Float#inspect
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0.004 0.001 0.000 0.002 109/109 PP::ObjectMixin#pretty_print
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0.003 0.001 0.000 0.001 109/109 PP::ObjectMixin#pretty_print
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0.003 0.002 0.000 0.000 317/317 PrettyPrint::GroupQueue#delete
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0.003 0.003 0.000 0.000 109/109 PP::ObjectMixin#pretty_print
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0.001 0.001 0.000 0.000 91/408 PrettyPrint::Breakable#initialize
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0.000 0.000 0.000 0.000 1/3 BioPieces::Fastq#get_entry
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0.003 0.000 0.000 0.002 1/1 Proc#call
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0.000 0.000 0.000 0.000 1/20 <Object::Object>#[]
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0.002 0.001 0.000 0.001 12/12 <Module::Marshal>#load
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0.002 0.001 0.000 0.002 12/12 Array#each
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0.002 0.002 0.000 0.000 109/109 PP::ObjectMixin#pretty_print
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--------------------------------------------------------------------------------
0.002 0.002 0.000 0.000 109/109 Method#call
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0.001 0.001 0.000 0.000 91/229 PrettyPrint::Breakable#output
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--------------------------------------------------------------------------------
0.002 0.002 0.000 0.000 109/109 PP::ObjectMixin#pretty_print
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0.001 0.001 0.000 0.000 19/128 Array#delete_if
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--------------------------------------------------------------------------------
0.002 0.002 0.000 0.000 317/317 PrettyPrint#group_sub
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0.001 0.000 0.000 0.001 1/1 BioPieces::Pipeline#run
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0.001 0.000 0.000 0.001 1/1 BioPieces::StatusHelper#status_init
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--------------------------------------------------------------------------------
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0.001 0.000 0.000 0.001 6/6 Tempfile#initialize
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0.001 0.001 0.000 0.000 155/155 PP::PPMethods#check_inspect_key
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0.001 0.001 0.000 0.000 83/83 PP::ObjectMixin#pretty_print
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0.00% 0.00% 0.001 0.001 0.000 0.000 23 Kernel#lambda
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 48/144 PrettyPrint#flush
0.001 0.001 0.000 0.000 96/144 Array#each
0.00% 0.00% 0.001 0.001 0.000 0.000 144 Array#clear
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/116 Time#strftime
0.000 0.000 0.000 0.000 12/116 Time#inspect
0.000 0.000 0.000 0.000 20/116 Time#_dump
0.000 0.000 0.000 0.000 72/116 <Class::Time>#_load
0.00% 0.00% 0.001 0.001 0.000 0.000 116 Fixnum#divmod
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.000 12/12 PP::ObjectMixin#pretty_print
0.00% 0.00% 0.001 0.001 0.000 0.000 12 Time#inspect
0.000 0.000 0.000 0.000 12/12 Integer#round
0.000 0.000 0.000 0.000 12/116 Fixnum#divmod
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.001 1/1 Global#[No method]
0.00% 0.00% 0.001 0.000 0.000 0.001 1 BioPieces::Commands#plot_scores
0.001 0.001 0.000 0.000 2/2 <Class::NArray>#int
0.000 0.000 0.000 0.000 1/2 BioPieces::OptionsHelper#options_files_exists_force
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed
0.000 0.000 0.000 0.000 2/7 BioPieces::OptionsHelper#options_allowed_values
0.000 0.000 0.000 0.000 1/371171 Class#new
0.000 0.000 0.000 0.000 1/6 Kernel#dup
0.000 0.000 0.000 0.000 1/6 Kernel#__method__
0.000 0.000 0.000 0.000 1/23 Kernel#lambda
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.000 1/1 Class#new
0.00% 0.00% 0.001 0.000 0.000 0.000 1 PrettyPrint#initialize
0.000 0.000 0.000 0.000 1/23 Kernel#lambda
0.000 0.000 0.000 0.000 2/371171 Class#new
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.000 64/64 Proc#call
0.00% 0.00% 0.001 0.001 0.000 0.000 64 String#*
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.000 5/5 Array#each
0.00% 0.00% 0.001 0.000 0.000 0.000 5 <Class::BioPieces::Stream>#pipe
0.000 0.000 0.000 0.000 5/5 <Class::IO>#pipe
0.000 0.000 0.000 0.000 10/371171 Class#new
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.000 2/2 BioPieces::Commands#plot_scores
0.00% 0.00% 0.001 0.001 0.000 0.000 2 <Class::NArray>#int
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.000 4/4 <Class::BioPieces::Filesys>#open
0.00% 0.00% 0.001 0.001 0.000 0.000 4 Regexp#===
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/48 Array#map
0.000 0.000 0.000 0.000 4/48 Hash#each_pair
0.000 0.000 0.000 0.000 12/48 BioPieces::Pipeline::Command#to_s
0.000 0.000 0.000 0.000 26/48 Hash#each
0.00% 0.00% 0.001 0.001 0.000 0.000 48 Symbol#to_s
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Global#[No method]
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Commands#read_fastq
0.000 0.000 0.000 0.000 2/6 BioPieces::OptionsHelper#options_assert
0.000 0.000 0.000 0.000 1/1 BioPieces::OptionsHelper#options_glob
0.000 0.000 0.000 0.000 1/2 BioPieces::OptionsHelper#options_files_exist
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed
0.000 0.000 0.000 0.000 1/6 Kernel#dup
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed_values
0.000 0.000 0.000 0.000 1/3 BioPieces::OptionsHelper#options_unique
0.000 0.000 0.000 0.000 1/371171 Class#new
0.000 0.000 0.000 0.000 1/1 BioPieces::OptionsHelper#options_required
0.000 0.000 0.000 0.000 1/23 Kernel#lambda
0.000 0.000 0.000 0.000 1/6 Kernel#__method__
0.000 0.000 0.000 0.000 1/1 Symbol#to_sym
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 PrettyPrint#nest
0.00% 0.00% 0.000 0.000 0.000 0.000 2 TrueClass#pretty_print
0.000 0.000 0.000 0.000 2/911 PrettyPrint#text
0.000 0.000 0.000 0.000 2/2 TrueClass#inspect
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/10 <Class::BioPieces::Filesys>#open
0.000 0.000 0.000 0.000 2/10 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/10 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 4/10 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 10 Kernel#respond_to?
0.000 0.000 0.000 0.000 9/1482651 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/15 BioPieces::Pipeline#to_s
0.000 0.000 0.000 0.000 1/15 Array#delete_if
0.000 0.000 0.000 0.000 12/15 BioPieces::Pipeline::Command#to_s
0.00% 0.00% 0.000 0.000 0.000 0.000 15 Array#join
0.000 0.000 0.000 0.000 3/15 Fixnum#to_s
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 49/49 Array#delete
0.00% 0.00% 0.000 0.000 0.000 0.000 49 BasicObject#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 3 NoMethodError#initialize
0.000 0.000 0.000 0.000 3/3 NameError#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/48 Time#_dump
0.000 0.000 0.000 0.000 36/48 <Class::Time>#_load
0.00% 0.00% 0.000 0.000 0.000 0.000 48 Fixnum#<=>
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 11/27 Integer#downto
0.000 0.000 0.000 0.000 16/27 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 27 PrettyPrint::Group#break
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/12 File#initialize
0.000 0.000 0.000 0.000 2/12 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/12 Delegator#method_missing
0.000 0.000 0.000 0.000 6/12 <Class::IO>#read
0.00% 0.00% 0.000 0.000 0.000 0.000 12 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 5/5 <Class::Thread>#new
0.00% 0.00% 0.000 0.000 0.000 0.000 5 Thread#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#create
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Dir::Tmpname#tmpdir
0.000 0.000 0.000 0.000 6/6 <Class::Dir>#tmpdir
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 5/5 <Class::BioPieces::Stream>#pipe
0.00% 0.00% 0.000 0.000 0.000 0.000 5 <Class::IO>#pipe
0.000 0.000 0.000 0.000 10/10 IO#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/10 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/12 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/33 BioPieces::StatusHelper#status_init
0.000 0.000 0.000 0.000 1/33 BioPieces::Pipeline#run_thread
0.000 0.000 0.000 0.000 11/33 Integer#downto
0.000 0.000 0.000 0.000 20/33 PrettyPrint#break_outmost_groups
0.00% 0.00% 0.000 0.000 0.000 0.000 33 Array#first
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 7/7 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 7 Exception#backtrace
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#tmpdir
0.00% 0.00% 0.000 0.000 0.000 0.000 6 <Class::Dir>#tmpdir
0.000 0.000 0.000 0.000 6/278 Array#each
0.000 0.000 0.000 0.000 18/20 <Object::Object>#[]
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 4/18 Array#to_s
0.000 0.000 0.000 0.000 14/18 PP::ObjectMixin#pretty_print
0.00% 0.00% 0.000 0.000 0.000 0.000 18 String#inspect
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#create
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Dir::Tmpname#make_tmpname
0.000 0.000 0.000 0.000 6/6 Time#strftime
0.000 0.000 0.000 0.000 6/8 <Class::Time>#now
0.000 0.000 0.000 0.000 6/6 Kernel#rand
0.000 0.000 0.000 0.000 12/15 Fixnum#to_s
0.000 0.000 0.000 0.000 6/632 Module#===
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 NoMethodError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 3 NameError#initialize
0.000 0.000 0.000 0.000 3/3 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 8/44 Time#initialize
0.000 0.000 0.000 0.000 36/44 <Class::Time>#_load
0.00% 0.00% 0.000 0.000 0.000 0.000 44 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Class#new
0.00% 0.00% 0.000 0.000 0.000 0.000 1 PrettyPrint::GroupQueue#initialize
0.000 0.000 0.000 0.000 1/278 Array#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 25/25 Numeric#pretty_print
0.00% 0.00% 0.000 0.000 0.000 0.000 25 Fixnum#inspect
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/43 Tempfile#initialize
0.000 0.000 0.000 0.000 1/43 Array#delete_if
0.000 0.000 0.000 0.000 36/43 Dir::Tmpname#create
0.00% 0.00% 0.000 0.000 0.000 0.000 43 <Class::Delegator>#const_missing
0.000 0.000 0.000 0.000 43/43 Module#const_get
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#mean_scores
0.000 0.000 0.000 0.000 3/6 BioPieces::Commands#trim_seq
0.000 0.000 0.000 0.000 2/6 BioPieces::Commands#read_fastq
0.00% 0.00% 0.000 0.000 0.000 0.000 6 BioPieces::OptionsHelper#options_assert
0.000 0.000 0.000 0.000 6/33 Hash#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/8 BioPieces::Pipeline::Command#run
0.000 0.000 0.000 0.000 6/8 Dir::Tmpname#make_tmpname
0.000 0.000 0.000 0.000 1/8 BioPieces::StatusHelper#status_track
0.00% 0.00% 0.000 0.000 0.000 0.000 8 <Class::Time>#now
0.000 0.000 0.000 0.000 8/8 Time#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/28 Array#each
0.000 0.000 0.000 0.000 22/28 Hash#each
0.00% 0.00% 0.000 0.000 0.000 0.000 28 Kernel#is_a?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Class#new
0.00% 0.00% 0.000 0.000 0.000 0.000 2 BioPieces::Filesys#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 11/11 Integer#downto
0.00% 0.00% 0.000 0.000 0.000 0.000 11 Array#slice!
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 Numeric#pretty_print
0.00% 0.00% 0.000 0.000 0.000 0.000 3 Float#inspect
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 8/8 <Class::Time>#now
0.00% 0.00% 0.000 0.000 0.000 0.000 8 Time#initialize
0.000 0.000 0.000 0.000 8/44 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Global#[No method]
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Commands#grab
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed
0.000 0.000 0.000 0.000 2/3 BioPieces::OptionsHelper#options_conflict
0.000 0.000 0.000 0.000 1/1 BioPieces::OptionsHelper#options_required_unique
0.000 0.000 0.000 0.000 1/6 Kernel#dup
0.000 0.000 0.000 0.000 1/3 BioPieces::OptionsHelper#options_unique
0.000 0.000 0.000 0.000 1/371171 Class#new
0.000 0.000 0.000 0.000 1/2 BioPieces::OptionsHelper#options_files_exist
0.000 0.000 0.000 0.000 1/23 Kernel#lambda
0.000 0.000 0.000 0.000 1/6 Kernel#__method__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Stream#close
0.000 0.000 0.000 0.000 1/7 IO#close
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/8 File#initialize
0.000 0.000 0.000 0.000 6/8 <Class::IO>#read
0.00% 0.00% 0.000 0.000 0.000 0.000 8 File#to_path
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#trim_seq
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#mean_scores
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#plot_scores
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#grab
0.000 0.000 0.000 0.000 1/7 BioPieces::Pipeline#run
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#read_fastq
0.00% 0.00% 0.000 0.000 0.000 0.000 7 BioPieces::OptionsHelper#options_allowed
0.000 0.000 0.000 0.000 7/7 Hash#each_key
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Global#[No method]
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/2 BioPieces::OptionsHelper#options_files_exists_force
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed
0.000 0.000 0.000 0.000 1/6 Kernel#dup
0.000 0.000 0.000 0.000 1/3 BioPieces::OptionsHelper#options_tie
0.000 0.000 0.000 0.000 1/3 BioPieces::OptionsHelper#options_unique
0.000 0.000 0.000 0.000 1/371171 Class#new
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed_values
0.000 0.000 0.000 0.000 1/23 Kernel#lambda
0.000 0.000 0.000 0.000 1/6 Kernel#__method__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/12 <Class::Time>#_load
0.00% 0.00% 0.000 0.000 0.000 0.000 12 Fixnum#*
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Range#each
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Seq#qual_base33?
0.000 0.000 0.000 0.000 1/370639 String#match
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 7/7 BioPieces::OptionsHelper#options_allowed
0.00% 0.00% 0.000 0.000 0.000 0.000 7 Hash#each_key
0.000 0.000 0.000 0.000 11/13 Array#include?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 NameError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 3 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 10/10 <Class::IO>#pipe
0.00% 0.00% 0.000 0.000 0.000 0.000 10 IO#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/12 Time#inspect
0.00% 0.00% 0.000 0.000 0.000 0.000 12 Integer#round
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#make_tmpname
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Time#strftime
0.000 0.000 0.000 0.000 12/116 Fixnum#divmod
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Class::BioPieces::Filesys>#open
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Kernel#block_given?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Fixnum#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/6 Hash#each_pair
0.000 0.000 0.000 0.000 4/6 Hash#each
0.00% 0.00% 0.000 0.000 0.000 0.000 6 TrueClass#to_s
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/20 BioPieces::LogHelper#log_ok
0.000 0.000 0.000 0.000 18/20 <Class::Dir>#tmpdir
0.000 0.000 0.000 0.000 1/20 BioPieces::HistoryHelper#history_save
0.00% 0.00% 0.000 0.000 0.000 0.000 20 <Object::Object>#[]
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Global#[No method]
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Commands#trim_seq
0.000 0.000 0.000 0.000 3/6 BioPieces::OptionsHelper#options_assert
0.000 0.000 0.000 0.000 1/371171 Class#new
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed_values
0.000 0.000 0.000 0.000 1/6 Kernel#dup
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed
0.000 0.000 0.000 0.000 1/23 Kernel#lambda
0.000 0.000 0.000 0.000 1/6 Kernel#__method__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 PP::PPMethods#guard_inspect_key
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Hash#==
0.000 0.000 0.000 0.000 2/1482651 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Global#[No method]
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Commands#mean_scores
0.000 0.000 0.000 0.000 1/6 BioPieces::OptionsHelper#options_assert
0.000 0.000 0.000 0.000 1/371171 Class#new
0.000 0.000 0.000 0.000 1/3 BioPieces::OptionsHelper#options_tie
0.000 0.000 0.000 0.000 1/6 Kernel#dup
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed_values
0.000 0.000 0.000 0.000 1/7 BioPieces::OptionsHelper#options_allowed
0.000 0.000 0.000 0.000 1/6 Kernel#__method__
0.000 0.000 0.000 0.000 1/23 Kernel#lambda
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 43/43 <Class::Delegator>#const_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 43 Module#const_get
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#read_fastq
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::OptionsHelper#options_glob
0.000 0.000 0.000 0.000 1/278 Array#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/13 Hash#each
0.000 0.000 0.000 0.000 11/13 Hash#each_key
0.00% 0.00% 0.000 0.000 0.000 0.000 13 Array#include?
0.000 0.000 0.000 0.000 22/2038581 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#trim_seq
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#mean_scores
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#plot_scores
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#grab
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#read_fastq
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Kernel#dup
0.000 0.000 0.000 0.000 6/6 Kernel#initialize_dup
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 PP::PPMethods#guard_inspect_key
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Kernel#taint
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#mean_scores
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#trim_seq
0.000 0.000 0.000 0.000 1/7 BioPieces::Pipeline#run
0.000 0.000 0.000 0.000 1/7 BioPieces::Commands#read_fastq
0.000 0.000 0.000 0.000 2/7 BioPieces::Commands#plot_scores
0.00% 0.00% 0.000 0.000 0.000 0.000 7 BioPieces::OptionsHelper#options_allowed_values
0.000 0.000 0.000 0.000 7/33 Hash#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Hash#each_pair
0.00% 0.00% 0.000 0.000 0.000 0.000 2 FalseClass#to_s
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/15 Dir::Tmpname#make_tmpname
0.000 0.000 0.000 0.000 3/15 Array#join
0.00% 0.00% 0.000 0.000 0.000 0.000 15 Fixnum#to_s
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 10/10 Class#new
0.00% 0.00% 0.000 0.000 0.000 0.000 10 BioPieces::Stream#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Tempfile#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Delegator#initialize
0.000 0.000 0.000 0.000 6/6 #<Class:0x007f8605e90f88>#__setobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 3 Exception#exception
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::Commands#grab
0.000 0.000 0.000 0.000 1/2 BioPieces::Commands#read_fastq
0.00% 0.00% 0.000 0.000 0.000 0.000 2 BioPieces::OptionsHelper#options_files_exist
0.000 0.000 0.000 0.000 2/278 Array#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 TrueClass#pretty_print
0.00% 0.00% 0.000 0.000 0.000 0.000 2 TrueClass#inspect
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Module::Marshal>#dump
0.00% 0.00% 0.000 0.000 0.000 0.000 2 IO#binmode
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/2 BioPieces::Commands#plot_scores
0.00% 0.00% 0.000 0.000 0.000 0.000 2 BioPieces::OptionsHelper#options_files_exists_force
0.000 0.000 0.000 0.000 2/278 Array#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Kernel#dup
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Kernel#initialize_dup
0.000 0.000 0.000 0.000 6/6 Hash#initialize_copy
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 6 <Class::File>#expand_path
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Delegator#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 6 #<Class:0x007f8605e90f88>#__setobj__
0.000 0.000 0.000 0.000 6/6 BasicObject#equal?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Hash#each
0.00% 0.00% 0.000 0.000 0.000 0.000 6 String#gsub!
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Array#delete_if
0.00% 0.00% 0.000 0.000 0.000 0.000 1 <Class::Regexp>#quote
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Class#new
0.00% 0.00% 0.000 0.000 0.000 0.000 6 BioPieces::Pipeline::Command#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#make_tmpname
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Kernel#rand
0.000 0.000 0.000 0.000 6/1482651 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 4/4 Hash#each
0.00% 0.00% 0.000 0.000 0.000 0.000 4 Array#to_s
0.000 0.000 0.000 0.000 4/18 String#inspect
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/3 BioPieces::Commands#grab
0.000 0.000 0.000 0.000 1/3 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/3 BioPieces::Commands#read_fastq
0.00% 0.00% 0.000 0.000 0.000 0.000 3 BioPieces::OptionsHelper#options_unique
0.000 0.000 0.000 0.000 3/278 Array#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 6 <Class::File>#stat
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/3 BioPieces::Pipeline#run
0.000 0.000 0.000 0.000 1/3 BioPieces::Commands#mean_scores
0.000 0.000 0.000 0.000 1/3 BioPieces::Commands#write_fastq
0.00% 0.00% 0.000 0.000 0.000 0.000 3 BioPieces::OptionsHelper#options_tie
0.000 0.000 0.000 0.000 3/33 Hash#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/3 BioPieces::Pipeline#run
0.000 0.000 0.000 0.000 2/3 BioPieces::Commands#grab
0.00% 0.00% 0.000 0.000 0.000 0.000 3 BioPieces::OptionsHelper#options_conflict
0.000 0.000 0.000 0.000 3/33 Hash#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Kernel#initialize_dup
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Hash#initialize_copy
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Class#new
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Tempfile::Remover#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 4/4 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 4 <Class::File>#file?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#create
0.00% 0.00% 0.000 0.000 0.000 0.000 6 <Class::File>#join
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 18/18 Dir::Tmpname#create
0.00% 0.00% 0.000 0.000 0.000 0.000 18 Fixnum#|
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 2 String#split
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Tempfile#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 6 <Module::ObjectSpace>#define_finalizer
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 6 File::Stat#writable?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#trim_seq
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#write_fastq
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#grab
0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#plot_scores
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0.000 0.000 0.000 0.000 1/6 BioPieces::Commands#mean_scores
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Kernel#__method__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#create
0.00% 0.00% 0.000 0.000 0.000 0.000 6 <Class::Hash>#try_convert
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#grab
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::OptionsHelper#options_required_unique
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Array#each
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::Pipeline#run_thread
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#read_fastq
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::OptionsHelper#options_required
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 6 File::Stat#directory?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#create
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Fixnum#~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Dir::Tmpname#create
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Array#each
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Tempfile#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 6 #<Module:0x007f8605e8a7f0>#block_given?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Class#new
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 #<Class:0x007f8605e90f88>#__setobj__
0.00% 0.00% 0.000 0.000 0.000 0.000 6 BasicObject#equal?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 2 IO#set_encoding
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Module#include
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 2 String#include?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 BioPieces::Pipeline#run_thread
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Array#[]
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Array#each
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#read_fastq
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--------------------------------------------------------------------------------
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* indicates recursively called methods
Thread ID: 70106804479800
Fiber ID: 70106804479660
Total Time: 1395.155480434
Sort by: total_time
%total %self total self wait child calls Name
--------------------------------------------------------------------------------
100.00% 0.00% 1395.155 0.000 0.000 1395.155 1 BioPieces::Pipeline#run_thread
1395.155 0.000 0.000 1395.155 1/1 BioPieces::Pipeline::Command#run
--------------------------------------------------------------------------------
1395.155 0.000 0.000 1395.155 1/1 BioPieces::Pipeline#run_thread
100.00% 0.00% 1395.155 0.000 0.000 1395.155 1 BioPieces::Pipeline::Command#run
1395.155 0.000 0.359 1394.796 1/2 Proc#call
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::StatusHelper#status_track
1395.155 0.000 0.359 1394.796 1/2 BioPieces::Pipeline::Command#run
100.00% 0.00% 1395.155 0.000 0.359 1394.796 2 *Proc#call
1394.791 0.000 0.000 1394.791 1/1 BioPieces::StatusHelper#status_track
1394.786 24.752 9.674 1360.360 1/1 BioPieces::Stream#each
0.005 0.000 0.000 0.005 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#compile_regexes
0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#compile_keys
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0.000 0.000 0.000 0.000 1/1 BioPieces::Commands#compile_lookup
0.000 0.000 0.000 0.000 1/1 Fixnum#*
--------------------------------------------------------------------------------
1394.791 0.000 0.000 1394.791 1/1 Proc#call
99.97% 0.00% 1394.791 0.000 0.000 1394.791 1 BioPieces::StatusHelper#status_track
0.004 0.000 0.000 0.004 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/2 Proc#call
--------------------------------------------------------------------------------
1394.786 24.752 9.674 1360.360 1/1 Proc#call
99.97% 1.77% 1394.786 24.752 9.674 1360.360 1 BioPieces::Stream#each
962.577 4.261 958.316 0.000 370639/370639 IO#eof?
235.275 7.606 0.000 227.669 79346/79346 BioPieces::Stream#write
124.341 25.089 2.609 96.643 370638/370638 BioPieces::Stream#read
38.167 9.484 0.190 28.492 370638/370638 BioPieces::Commands#grab_regexes
--------------------------------------------------------------------------------
962.577 4.261 958.316 0.000 370639/370639 BioPieces::Stream#each
68.99% 0.31% 962.577 4.261 958.316 0.000 370639 IO#eof?
--------------------------------------------------------------------------------
235.275 7.606 0.000 227.669 79346/79346 BioPieces::Stream#each
16.86% 0.55% 235.275 7.606 0.000 227.669 79346 BioPieces::Stream#write
219.613 5.968 213.645 0.000 158692/158694 IO#write
7.212 3.899 1.510 1.803 79346/79346 <Module::MessagePack>#pack
0.844 0.844 0.000 0.000 79346/79346 Array#pack
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/158694 <Module::Marshal>#dump
219.613 5.968 213.645 0.000 158692/158694 BioPieces::Stream#write
15.74% 0.43% 219.613 5.968 213.645 0.000 158694 IO#write
--------------------------------------------------------------------------------
124.341 25.089 2.609 96.643 370638/370638 BioPieces::Stream#each
8.91% 1.80% 124.341 25.089 2.609 96.643 370638 BioPieces::Stream#read
50.386 8.954 41.432 0.000 741276/741276 IO#read
41.154 22.086 10.535 8.533 370638/370638 <Module::MessagePack>#unpack
2.940 2.940 0.000 0.000 370638/370638 String#unpack
2.163 2.163 0.000 0.000 370638/370638 Array#first
--------------------------------------------------------------------------------
50.386 8.954 41.432 0.000 741276/741276 BioPieces::Stream#read
3.61% 0.64% 50.386 8.954 41.432 0.000 741276 IO#read
--------------------------------------------------------------------------------
41.154 22.086 10.535 8.533 370638/370638 BioPieces::Stream#read
2.95% 1.58% 41.154 22.086 10.535 8.533 370638 <Module::MessagePack>#unpack
8.533 8.533 0.000 0.000 1482552/1800000 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
38.167 9.484 0.190 28.492 370638/370638 BioPieces::Stream#each
2.74% 0.68% 38.167 9.484 0.190 28.492 370638 BioPieces::Commands#grab_regexes
28.492 8.765 0.204 19.523 370638/741277 Array#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 370638/741277 Array#each
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28.492 8.765 0.204 19.523 370638/741277 BioPieces::Commands#grab_regexes
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5.736 5.736 0.000 0.000 370638/370638 String#=~
0.000 0.000 0.000 0.000 1/1 Class#new
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/1800000 Kernel#respond_to?
0.000 0.000 0.000 0.000 58/1800000 <Module::Marshal>#dump
1.803 1.803 0.000 0.000 317384/1800000 <Module::MessagePack>#pack
8.533 8.533 0.000 0.000 1482552/1800000 <Module::MessagePack>#unpack
0.74% 0.74% 10.337 10.337 0.000 0.000 1800000 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
7.212 3.899 1.510 1.803 79346/79346 BioPieces::Stream#write
0.52% 0.28% 7.212 3.899 1.510 1.803 79346 <Module::MessagePack>#pack
1.803 1.803 0.000 0.000 317384/1800000 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
5.736 5.736 0.000 0.000 370638/370638 Array#each
0.41% 0.41% 5.736 5.736 0.000 0.000 370638 String#=~
--------------------------------------------------------------------------------
2.940 2.940 0.000 0.000 370638/370638 BioPieces::Stream#read
0.21% 0.21% 2.940 2.940 0.000 0.000 370638 String#unpack
--------------------------------------------------------------------------------
2.163 2.163 0.000 0.000 370638/370638 BioPieces::Stream#read
0.16% 0.16% 2.163 2.163 0.000 0.000 370638 Array#first
--------------------------------------------------------------------------------
0.844 0.844 0.000 0.000 79346/79346 BioPieces::Stream#write
0.06% 0.06% 0.844 0.844 0.000 0.000 79346 Array#pack
--------------------------------------------------------------------------------
0.004 0.000 0.000 0.004 1/2 BioPieces::StatusHelper#status_track
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0.00% 0.00% 0.009 0.000 0.000 0.009 2 BioPieces::StatusHelper#status_save
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0.000 0.000 0.000 0.000 2/2 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
--------------------------------------------------------------------------------
0.005 0.000 0.000 0.005 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.005 0.000 0.000 0.005 2 <Class::IO>#open
0.005 0.000 0.000 0.005 2/4 File#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/4 Delegator#method_missing
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0.002 0.001 0.000 0.002 2/2 Delegator#method_missing
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0.000 0.000 0.000 0.000 2/2 File#to_path
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.001 34/36 Hash#each
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0.00% 0.00% 0.004 0.002 0.000 0.002 36 <Module::Marshal>#dump
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0.000 0.000 0.000 0.000 2/2 IO#binmode
--------------------------------------------------------------------------------
0.004 0.001 0.000 0.002 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.004 0.001 0.000 0.002 2 Hash#each
0.002 0.001 0.000 0.001 34/36 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 36/36 Symbol#==
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.002 2/2 File#initialize
0.00% 0.00% 0.002 0.001 0.000 0.002 2 Delegator#method_missing
0.001 0.000 0.000 0.001 2/2 BasicObject#method_missing
0.000 0.000 0.000 0.000 2/2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Kernel#respond_to?
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0.000 0.000 0.000 0.000 2/4 File#initialize
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.000 6/6 <Module::Marshal>#dump
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0.000 0.000 0.000 0.000 6/6 Fixnum#==
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.001 2/2 Delegator#method_missing
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0.000 0.000 0.000 0.000 2/2 Exception#exception
--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 BasicObject#method_missing
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 20/20 Time#_dump
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Time#_dump
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NameError#initialize
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/3 BioPieces::Commands#compile_patterns
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Fixnum#to_f
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#exception
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Commands#compile_lookup
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Fixnum#*
* indicates recursively called methods
Thread ID: 70106804480060
Fiber ID: 70106804479240
Total Time: 1395.154262438
Sort by: total_time
%total %self total self wait child calls Name
--------------------------------------------------------------------------------
100.00% 0.00% 1395.154 0.000 0.000 1395.154 1 BioPieces::Pipeline#run_thread
1395.154 0.000 0.000 1395.154 1/1 BioPieces::Pipeline::Command#run
--------------------------------------------------------------------------------
1395.154 0.000 0.000 1395.154 1/1 BioPieces::Pipeline#run_thread
100.00% 0.00% 1395.154 0.000 0.000 1395.154 1 BioPieces::Pipeline::Command#run
1395.154 0.001 0.283 1394.870 1/2 Proc#call
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::StatusHelper#status_track
1395.154 0.001 0.283 1394.870 1/2 BioPieces::Pipeline::Command#run
100.00% 0.00% 1395.154 0.001 0.283 1394.870 2 *Proc#call
1394.866 0.000 0.000 1394.865 1/1 BioPieces::StatusHelper#status_track
1394.795 13.855 2.828 1378.112 1/1 BioPieces::Stream#each
0.064 0.000 0.000 0.064 1/1 <Module::Gnuplot>#open
0.005 0.000 0.000 0.005 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 3/158695 NArray#[]
0.000 0.000 0.000 0.000 1/1 Enumerable#to_a
0.000 0.000 0.000 0.000 2/2 NArray#to_a
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
0.000 0.000 0.000 0.000 1/1 NArray#max
0.000 0.000 0.000 0.000 1/1 NArray#*
0.000 0.000 0.000 0.000 1/1 NArray#/
0.000 0.000 0.000 0.000 2/2 NArray#to_f
0.000 0.000 0.000 0.000 1/1 Float#to_f
0.000 0.000 0.000 0.000 1/1 <Class::NArray>#sfloat
0.000 0.000 0.000 0.000 1/1 Fixnum#/
--------------------------------------------------------------------------------
1394.866 0.000 0.000 1394.865 1/1 Proc#call
99.98% 0.00% 1394.866 0.000 0.000 1394.865 1 BioPieces::StatusHelper#status_track
0.006 0.000 0.000 0.005 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/2 Proc#call
--------------------------------------------------------------------------------
1394.795 13.855 2.828 1378.112 1/1 Proc#call
99.97% 0.99% 1394.795 13.855 2.828 1378.112 1 BioPieces::Stream#each
1096.907 1.545 1095.361 0.000 79347/79347 IO#eof?
216.981 7.598 0.000 209.382 79346/79346 BioPieces::Stream#write
30.433 6.001 1.197 23.235 79346/79346 BioPieces::Stream#read
11.739 6.754 2.016 2.968 158692/158695 NArray#[]
10.732 5.075 2.767 2.889 158692/158692 NArray#[]=
6.136 4.856 0.755 0.525 158692/158692 NArray#+
4.196 2.702 0.948 0.545 79346/79346 NArray#-
0.989 0.989 0.000 0.000 79346/79346 <Class::NArray>#to_na
--------------------------------------------------------------------------------
1096.907 1.545 1095.361 0.000 79347/79347 BioPieces::Stream#each
78.62% 0.11% 1096.907 1.545 1095.361 0.000 79347 IO#eof?
--------------------------------------------------------------------------------
216.981 7.598 0.000 209.382 79346/79346 BioPieces::Stream#each
15.55% 0.54% 216.981 7.598 0.000 209.382 79346 BioPieces::Stream#write
202.050 5.813 196.238 0.000 158692/158696 IO#write
6.477 3.529 1.140 1.809 79346/79346 <Module::MessagePack>#pack
0.855 0.855 0.000 0.000 79346/79346 Array#pack
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/158696 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 2/158696 IO#<<
202.050 5.813 196.238 0.000 158692/158696 BioPieces::Stream#write
14.48% 0.42% 202.051 5.813 196.238 0.000 158696 IO#write
--------------------------------------------------------------------------------
30.433 6.001 1.197 23.235 79346/79346 BioPieces::Stream#each
2.18% 0.43% 30.433 6.001 1.197 23.235 79346 BioPieces::Stream#read
13.011 2.605 10.406 0.000 158692/158693 IO#read
9.000 5.084 2.043 1.873 79346/79346 <Module::MessagePack>#unpack
0.733 0.733 0.000 0.000 79346/79346 String#unpack
0.491 0.491 0.000 0.000 79346/79346 Array#first
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/158693 <Class::IO>#popen
13.011 2.605 10.406 0.000 158692/158693 BioPieces::Stream#read
0.93% 0.19% 13.011 2.605 10.406 0.000 158693 IO#read
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/158695 Proc#call
11.739 6.754 2.016 2.968 158692/158695 BioPieces::Stream#each
0.84% 0.48% 11.739 6.754 2.016 2.968 158695 NArray#[]
1.054 1.054 0.000 0.000 158695/317387 Range#begin
0.959 0.959 0.000 0.000 158695/317387 Range#end
0.955 0.955 0.000 0.000 158695/317387 Range#exclude_end?
--------------------------------------------------------------------------------
10.732 5.075 2.767 2.889 158692/158692 BioPieces::Stream#each
0.77% 0.36% 10.732 5.075 2.767 2.889 158692 NArray#[]=
0.995 0.995 0.000 0.000 158692/317387 Range#begin
0.952 0.952 0.000 0.000 158692/317387 Range#end
0.943 0.943 0.000 0.000 158692/317387 Range#exclude_end?
--------------------------------------------------------------------------------
9.000 5.084 2.043 1.873 79346/79346 BioPieces::Stream#read
0.65% 0.36% 9.000 5.084 2.043 1.873 79346 <Module::MessagePack>#unpack
1.873 1.873 0.000 0.000 317384/634856 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
6.477 3.529 1.140 1.809 79346/79346 BioPieces::Stream#write
0.46% 0.25% 6.477 3.529 1.140 1.809 79346 <Module::MessagePack>#pack
1.809 1.809 0.000 0.000 317384/634856 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
6.136 4.856 0.755 0.525 158692/158692 BioPieces::Stream#each
0.44% 0.35% 6.136 4.856 0.755 0.525 158692 NArray#+
0.525 0.525 0.000 0.000 79346/158693 Module#<=
--------------------------------------------------------------------------------
4.196 2.702 0.948 0.545 79346/79346 BioPieces::Stream#each
0.30% 0.19% 4.196 2.702 0.948 0.545 79346 NArray#-
0.545 0.545 0.000 0.000 79346/158693 Module#<=
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/634856 Kernel#respond_to?
0.001 0.001 0.000 0.000 82/634856 <Module::Marshal>#dump
1.809 1.809 0.000 0.000 317384/634856 <Module::MessagePack>#pack
1.873 1.873 0.000 0.000 317384/634856 <Module::MessagePack>#unpack
0.26% 0.26% 3.683 3.683 0.000 0.000 634856 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.995 0.995 0.000 0.000 158692/317387 NArray#[]=
1.054 1.054 0.000 0.000 158695/317387 NArray#[]
0.15% 0.15% 2.050 2.050 0.000 0.000 317387 Range#begin
--------------------------------------------------------------------------------
0.952 0.952 0.000 0.000 158692/317387 NArray#[]=
0.959 0.959 0.000 0.000 158695/317387 NArray#[]
0.14% 0.14% 1.910 1.910 0.000 0.000 317387 Range#end
--------------------------------------------------------------------------------
0.943 0.943 0.000 0.000 158692/317387 NArray#[]=
0.955 0.955 0.000 0.000 158695/317387 NArray#[]
0.14% 0.14% 1.898 1.898 0.000 0.000 317387 Range#exclude_end?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/158693 NArray#*
0.525 0.525 0.000 0.000 79346/158693 NArray#+
0.545 0.545 0.000 0.000 79346/158693 NArray#-
0.08% 0.08% 1.070 1.070 0.000 0.000 158693 Module#<=
--------------------------------------------------------------------------------
0.989 0.989 0.000 0.000 79346/79346 BioPieces::Stream#each
0.07% 0.07% 0.989 0.989 0.000 0.000 79346 <Class::NArray>#to_na
--------------------------------------------------------------------------------
0.855 0.855 0.000 0.000 79346/79346 BioPieces::Stream#write
0.06% 0.06% 0.855 0.855 0.000 0.000 79346 Array#pack
--------------------------------------------------------------------------------
0.733 0.733 0.000 0.000 79346/79346 BioPieces::Stream#read
0.05% 0.05% 0.733 0.733 0.000 0.000 79346 String#unpack
--------------------------------------------------------------------------------
0.491 0.491 0.000 0.000 79346/79346 BioPieces::Stream#read
0.04% 0.04% 0.491 0.491 0.000 0.000 79346 Array#first
--------------------------------------------------------------------------------
0.064 0.000 0.000 0.064 1/1 Proc#call
0.00% 0.00% 0.064 0.000 0.000 0.064 1 <Module::Gnuplot>#open
0.060 0.024 0.000 0.036 1/1 <Class::IO>#popen
0.004 0.000 0.000 0.004 1/1 <Module::Gnuplot>#gnuplot
--------------------------------------------------------------------------------
0.060 0.024 0.000 0.036 1/1 <Module::Gnuplot>#open
0.00% 0.00% 0.060 0.024 0.000 0.036 1 <Class::IO>#popen
0.035 0.000 0.000 0.035 1/2 Class#new
0.000 0.000 0.000 0.000 1/158693 IO#read
0.000 0.000 0.000 0.000 1/5 IO#close
0.000 0.000 0.000 0.000 1/1 IO#close_write
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 Gnuplot::Plot#initialize
0.035 0.000 0.000 0.035 1/2 <Class::IO>#popen
0.00% 0.00% 0.035 0.000 0.000 0.035 2 *Class#new
0.035 0.001 0.000 0.034 1/1 Gnuplot::Plot#initialize
0.000 0.000 0.000 0.000 1/1 Gnuplot::DataSet#initialize
--------------------------------------------------------------------------------
0.035 0.001 0.000 0.034 1/1 Class#new
0.00% 0.00% 0.035 0.001 0.000 0.034 1 Gnuplot::Plot#initialize
0.023 0.000 0.000 0.023 1/1 Gnuplot::Plot#store_datasets
0.003 0.000 0.000 0.003 1/1 Enumerable#min
0.003 0.000 0.000 0.003 1/1 Enumerable#max
0.003 0.000 0.000 0.002 10/10 Gnuplot::Plot#method_missing
0.002 0.000 0.000 0.001 1/1 Gnuplot::Plot#to_gplot
0.000 0.000 0.000 0.000 2/2 IO#<<
0.000 0.000 0.000 0.000 4/255 Fixnum#to_s
0.000 0.000 0.000 0.000 1/2 Kernel#block_given?
0.000 0.000 0.000 0.000 1/2 Class#new
--------------------------------------------------------------------------------
0.023 0.000 0.000 0.023 1/1 Gnuplot::Plot#initialize
0.00% 0.00% 0.023 0.000 0.000 0.023 1 Gnuplot::Plot#store_datasets
0.022 0.000 0.000 0.022 2/3 Array#collect
0.000 0.000 0.000 0.000 2/264 Array#join
0.000 0.000 0.000 0.000 1/1 Array#compact
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/3 Array#to_gplot
0.022 0.000 0.000 0.022 2/3 Gnuplot::Plot#store_datasets
0.00% 0.00% 0.022 0.000 0.000 0.022 3 *Array#collect
0.022 0.000 0.000 0.022 1/1 Gnuplot::DataSet#to_gplot
0.017 0.010 0.000 0.007 251/264 Array#join
0.001 0.000 0.000 0.000 1/1 Gnuplot::DataSet#plot_args
--------------------------------------------------------------------------------
0.022 0.000 0.000 0.022 1/1 Array#collect
0.00% 0.00% 0.022 0.000 0.000 0.022 1 Gnuplot::DataSet#to_gplot
0.022 0.000 0.000 0.021 1/1 Array#to_gplot
0.000 0.000 0.000 0.000 1/1 Module#===
0.000 0.000 0.000 0.000 1/2 Kernel#===
--------------------------------------------------------------------------------
0.022 0.000 0.000 0.021 1/1 Gnuplot::DataSet#to_gplot
0.00% 0.00% 0.022 0.000 0.000 0.021 1 Array#to_gplot
0.000 0.000 0.000 0.000 1/264 Array#join
0.000 0.000 0.000 0.000 1/1 Array#zip
0.000 0.000 0.000 0.000 3/3 Array#[]
0.000 0.000 0.000 0.000 1/1 Kernel#kind_of?
0.000 0.000 0.000 0.000 1/3 Array#collect
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/264 Gnuplot::Plot#store_datasets
0.000 0.000 0.000 0.000 10/264 Array#each
0.000 0.000 0.000 0.000 1/264 Array#to_gplot
0.017 0.010 0.000 0.007 251/264 Array#collect
0.00% 0.00% 0.018 0.010 0.000 0.007 264 Array#join
0.005 0.005 0.000 0.000 251/251 Float#to_s
0.002 0.002 0.000 0.000 251/255 Fixnum#to_s
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/7 <Module::Gnuplot>#which_helper
0.001 0.000 0.000 0.001 2/7 Gnuplot::Plot#to_gplot
0.003 0.002 0.000 0.002 1/7 Enumerable#max
0.003 0.002 0.000 0.002 1/7 Enumerable#min
0.004 0.000 0.000 0.004 1/7 <Module::Gnuplot>#which
0.00% 0.00% 0.012 0.004 0.000 0.008 7 *Array#each
0.004 0.000 0.000 0.004 2/2 <Module::Gnuplot>#which_helper
0.003 0.003 0.000 0.000 500/512 Fixnum#<=>
0.002 0.002 0.000 0.000 22/24 <Class::File>#executable?
0.001 0.000 0.000 0.000 10/10 Array#map
0.000 0.000 0.000 0.000 22/22 <Class::File>#join
0.000 0.000 0.000 0.000 10/264 Array#join
0.000 0.000 0.000 0.000 22/22 String#strip
0.000 0.000 0.000 0.000 10/10 Symbol#to_proc
--------------------------------------------------------------------------------
0.005 0.000 0.000 0.005 1/2 Proc#call
0.006 0.000 0.000 0.005 1/2 BioPieces::StatusHelper#status_track
0.00% 0.00% 0.010 0.000 0.000 0.010 2 BioPieces::StatusHelper#status_save
0.006 0.000 0.000 0.006 2/2 <Class::IO>#open
0.004 0.001 0.000 0.003 2/2 Hash#each
0.000 0.000 0.000 0.000 2/2 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
--------------------------------------------------------------------------------
0.006 0.000 0.000 0.006 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.006 0.000 0.000 0.006 2 <Class::IO>#open
0.006 0.000 0.000 0.006 2/4 File#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/4 Delegator#method_missing
0.006 0.000 0.000 0.006 2/4 <Class::IO>#open
0.00% 0.00% 0.006 0.000 0.000 0.006 4 *File#initialize
0.003 0.001 0.000 0.003 2/2 Delegator#method_missing
0.002 0.001 0.000 0.001 2/28 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 2/5 IO#close
0.000 0.000 0.000 0.000 2/2 File#to_path
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.005 0.005 0.000 0.000 251/251 Array#join
0.00% 0.00% 0.005 0.005 0.000 0.000 251 Float#to_s
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.001 2/28 File#initialize
0.003 0.002 0.000 0.001 26/28 Hash#each
0.00% 0.00% 0.005 0.003 0.000 0.002 28 <Module::Marshal>#dump
0.001 0.001 0.000 0.001 6/6 Time#_dump
0.001 0.001 0.000 0.000 82/634856 Kernel#respond_to_missing?
0.000 0.000 0.000 0.000 2/158696 IO#write
0.000 0.000 0.000 0.000 2/2 IO#binmode
--------------------------------------------------------------------------------
0.004 0.000 0.000 0.004 1/1 <Module::Gnuplot>#open
0.00% 0.00% 0.004 0.000 0.000 0.004 1 <Module::Gnuplot>#gnuplot
0.004 0.000 0.000 0.004 1/1 <Module::Gnuplot>#which
0.000 0.000 0.000 0.000 1/3 <Object::Object>#[]
--------------------------------------------------------------------------------
0.004 0.000 0.000 0.004 1/1 <Module::Gnuplot>#gnuplot
0.00% 0.00% 0.004 0.000 0.000 0.004 1 <Module::Gnuplot>#which
0.004 0.000 0.000 0.004 1/7 Array#each
--------------------------------------------------------------------------------
0.004 0.000 0.000 0.004 2/2 Array#each
0.00% 0.00% 0.004 0.000 0.000 0.004 2 <Module::Gnuplot>#which_helper
0.000 0.000 0.000 0.000 2/24 <Class::File>#executable?
0.000 0.000 0.000 0.000 2/2 String#split
0.000 0.000 0.000 0.000 2/3 <Object::Object>#[]
0.000 0.000 0.000 0.000 2/7 Array#each
--------------------------------------------------------------------------------
0.004 0.001 0.000 0.003 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.004 0.001 0.000 0.003 2 Hash#each
0.003 0.002 0.000 0.001 26/28 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 28/28 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/512 Time#_dump
0.003 0.003 0.000 0.000 500/512 Array#each
0.00% 0.00% 0.003 0.003 0.000 0.000 512 Fixnum#<=>
--------------------------------------------------------------------------------
0.003 0.000 0.000 0.003 1/1 Gnuplot::Plot#initialize
0.00% 0.00% 0.003 0.000 0.000 0.003 1 Enumerable#min
0.003 0.002 0.000 0.002 1/7 Array#each
--------------------------------------------------------------------------------
0.003 0.001 0.000 0.003 2/2 File#initialize
0.00% 0.00% 0.003 0.001 0.000 0.003 2 Delegator#method_missing
0.002 0.000 0.000 0.001 2/2 BasicObject#method_missing
0.000 0.000 0.000 0.000 2/2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
0.000 0.000 0.000 0.000 2/4 File#initialize
--------------------------------------------------------------------------------
0.003 0.000 0.000 0.003 1/1 Gnuplot::Plot#initialize
0.00% 0.00% 0.003 0.000 0.000 0.003 1 Enumerable#max
0.003 0.002 0.000 0.002 1/7 Array#each
--------------------------------------------------------------------------------
0.003 0.000 0.000 0.002 10/10 Gnuplot::Plot#initialize
0.00% 0.00% 0.003 0.000 0.000 0.002 10 Gnuplot::Plot#method_missing
0.002 0.001 0.000 0.001 10/10 Gnuplot::Plot#set
0.000 0.000 0.000 0.000 10/10 Symbol#id2name
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/24 <Module::Gnuplot>#which_helper
0.002 0.002 0.000 0.000 22/24 Array#each
0.00% 0.00% 0.002 0.002 0.000 0.000 24 <Class::File>#executable?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 4/255 Gnuplot::Plot#initialize
0.002 0.002 0.000 0.000 251/255 Array#join
0.00% 0.00% 0.002 0.002 0.000 0.000 255 Fixnum#to_s
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.001 10/10 Gnuplot::Plot#method_missing
0.00% 0.00% 0.002 0.001 0.000 0.001 10 Gnuplot::Plot#set
0.001 0.001 0.000 0.000 10/10 Array#include?
0.000 0.000 0.000 0.000 1/1 Symbol#=~
--------------------------------------------------------------------------------
0.002 0.000 0.000 0.001 2/2 Delegator#method_missing
0.00% 0.00% 0.002 0.000 0.000 0.001 2 BasicObject#method_missing
0.001 0.000 0.000 0.000 2/2 Array#delete_if
0.000 0.000 0.000 0.000 6/6 Exception#backtrace
0.000 0.000 0.000 0.000 2/2 NoMethodError#initialize
0.000 0.000 0.000 0.000 2/2 Exception#exception
--------------------------------------------------------------------------------
0.002 0.000 0.000 0.001 1/1 Gnuplot::Plot#initialize
0.00% 0.00% 0.002 0.000 0.000 0.001 1 Gnuplot::Plot#to_gplot
0.001 0.000 0.000 0.001 2/7 Array#each
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.000 10/10 Gnuplot::Plot#set
0.00% 0.00% 0.001 0.001 0.000 0.000 10 Array#include?
0.000 0.000 0.000 0.000 65/65 String#==
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.001 6/6 <Module::Marshal>#dump
0.00% 0.00% 0.001 0.001 0.000 0.001 6 Time#_dump
0.000 0.000 0.000 0.000 20/20 Fixnum#divmod
0.000 0.000 0.000 0.000 12/512 Fixnum#<=>
0.000 0.000 0.000 0.000 6/6 Fixnum#==
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.000 10/10 Array#each
0.00% 0.00% 0.001 0.000 0.000 0.000 10 Array#map
0.000 0.000 0.000 0.000 19/19 String#to_s
0.000 0.000 0.000 0.000 11/11 Symbol#to_s
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.001 0.000 0.000 0.000 2 Array#delete_if
0.000 0.000 0.000 0.000 15/15 Regexp#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/5 BioPieces::Stream#close
0.000 0.000 0.000 0.000 1/5 <Class::IO>#popen
0.000 0.000 0.000 0.000 2/5 File#initialize
0.00% 0.00% 0.001 0.001 0.000 0.000 5 IO#close
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.000 1/1 Array#collect
0.00% 0.00% 0.001 0.000 0.000 0.000 1 Gnuplot::DataSet#plot_args
0.000 0.000 0.000 0.000 1/1 Regexp#===
0.000 0.000 0.000 0.000 1/2 Kernel#===
0.000 0.000 0.000 0.000 1/1 Kernel#instance_of?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 65/65 Array#include?
0.00% 0.00% 0.000 0.000 0.000 0.000 65 String#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Exception#backtrace
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 22/22 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 22 <Class::File>#join
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/8 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 2/8 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 8 Kernel#respond_to?
0.000 0.000 0.000 0.000 6/634856 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Gnuplot::Plot#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 IO#<<
0.000 0.000 0.000 0.000 2/158696 IO#write
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 15/15 Array#delete_if
0.00% 0.00% 0.000 0.000 0.000 0.000 15 Regexp#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NoMethodError#initialize
0.000 0.000 0.000 0.000 2/2 NameError#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/6 File#initialize
0.000 0.000 0.000 0.000 2/6 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/6 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 28/28 Hash#each
0.00% 0.00% 0.000 0.000 0.000 0.000 28 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Class#new
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Gnuplot::DataSet#initialize
0.000 0.000 0.000 0.000 1/2 Kernel#block_given?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 20/20 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 20 Fixnum#divmod
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 22/22 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 22 String#strip
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::Pipeline::Command#run
0.000 0.000 0.000 0.000 1/2 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 2 <Class::Time>#now
0.000 0.000 0.000 0.000 2/2 Time#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Array#to_gplot
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Array#zip
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.000 0.000 0.000 0.000 2 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/5 IO#close
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 19/19 Array#map
0.00% 0.00% 0.000 0.000 0.000 0.000 19 String#to_s
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NoMethodError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NameError#initialize
0.000 0.000 0.000 0.000 2/2 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Gnuplot::DataSet#plot_args
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Regexp#===
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 Gnuplot::DataSet#to_gplot
0.000 0.000 0.000 0.000 1/2 Gnuplot::DataSet#plot_args
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Kernel#===
0.000 0.000 0.000 0.000 2/2 BasicObject#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 10/10 Array#each
0.00% 0.00% 0.000 0.000 0.000 0.000 10 Symbol#to_proc
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 10/10 Gnuplot::Plot#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 10 Symbol#id2name
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Fixnum#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 11/11 Array#map
0.00% 0.00% 0.000 0.000 0.000 0.000 11 Symbol#to_s
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Class::Time>#now
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Time#initialize
0.000 0.000 0.000 0.000 2/2 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Enumerable#to_a
0.000 0.000 0.000 0.000 1/1 Range#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NArray#to_a
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Module::Gnuplot>#which_helper
0.00% 0.00% 0.000 0.000 0.000 0.000 2 String#split
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Gnuplot::Plot#set
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Symbol#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Enumerable#to_a
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Range#each
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NameError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 <Class::IO>#popen
0.00% 0.00% 0.000 0.000 0.000 0.000 1 IO#close_write
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 Gnuplot::DataSet#initialize
0.000 0.000 0.000 0.000 1/2 Gnuplot::Plot#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Kernel#block_given?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Module::Marshal>#dump
0.00% 0.00% 0.000 0.000 0.000 0.000 2 IO#binmode
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Kernel#===
0.00% 0.00% 0.000 0.000 0.000 0.000 2 BasicObject#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/3 <Module::Gnuplot>#gnuplot
0.000 0.000 0.000 0.000 2/3 <Module::Gnuplot>#which_helper
0.00% 0.00% 0.000 0.000 0.000 0.000 3 <Object::Object>#[]
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#exception
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 NArray#max
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 File#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 File#to_path
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 NArray#*
0.000 0.000 0.000 0.000 1/158693 Module#<=
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 Array#to_gplot
0.00% 0.00% 0.000 0.000 0.000 0.000 3 Array#[]
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Gnuplot::Plot#store_datasets
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Array#compact
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Gnuplot::DataSet#plot_args
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Kernel#instance_of?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 NArray#/
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NArray#to_f
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Time#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Gnuplot::DataSet#to_gplot
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Module#===
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Array#to_gplot
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Kernel#kind_of?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Float#to_f
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 <Class::NArray>#sfloat
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Fixnum#/
* indicates recursively called methods
Thread ID: 70106804480340
Fiber ID: 70106804479140
Total Time: 1395.153696957
Sort by: total_time
%total %self total self wait child calls Name
--------------------------------------------------------------------------------
100.00% 0.00% 1395.154 0.000 0.000 1395.154 1 BioPieces::Pipeline#run_thread
1395.154 0.000 0.000 1395.154 1/1 BioPieces::Pipeline::Command#run
--------------------------------------------------------------------------------
1395.154 0.000 0.000 1395.154 1/1 BioPieces::Pipeline#run_thread
100.00% 0.00% 1395.154 0.000 0.000 1395.154 1 BioPieces::Pipeline::Command#run
1395.153 0.000 0.272 1394.882 1/2 Proc#call
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::StatusHelper#status_track
1395.153 0.000 0.272 1394.882 1/2 BioPieces::Pipeline::Command#run
100.00% 0.00% 1395.153 0.000 0.272 1394.882 2 *Proc#call
1394.877 0.000 0.000 1394.877 1/1 BioPieces::StatusHelper#status_track
1394.829 0.000 0.000 1394.828 1/1 <Class::BioPieces::Filesys>#open
0.005 0.000 0.000 0.005 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 4/4 IO#set_encoding
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
0.000 0.000 0.000 0.000 1/1 Module#include
0.000 0.000 0.000 0.000 8/8 Module#method_added
0.000 0.000 0.000 0.000 1/1 String#===
0.000 0.000 0.000 0.000 4/4 Class#inherited
0.000 0.000 0.000 0.000 3/3 BasicObject#singleton_method_added
--------------------------------------------------------------------------------
1394.877 0.000 0.000 1394.877 1/1 Proc#call
99.98% 0.00% 1394.877 0.000 0.000 1394.877 1 BioPieces::StatusHelper#status_track
0.005 0.000 0.000 0.005 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/2 Proc#call
--------------------------------------------------------------------------------
1394.829 0.000 0.000 1394.828 1/1 Proc#call
99.98% 0.00% 1394.829 0.000 0.000 1394.828 1 <Class::BioPieces::Filesys>#open
1394.762 8.997 3.737 1382.029 1/1 BioPieces::Stream#each
0.065 0.000 0.000 0.065 1/3 <Class::IO>#open
0.000 0.000 0.000 0.000 1/79347 Class#new
0.000 0.000 0.000 0.000 1/4 IO#close
0.000 0.000 0.000 0.000 1/1 Kernel#block_given?
0.000 0.000 0.000 0.000 3/3 Array#shift
0.000 0.000 0.000 0.000 3/3 Symbol#===
--------------------------------------------------------------------------------
1394.762 8.997 3.737 1382.029 1/1 <Class::BioPieces::Filesys>#open
99.97% 0.64% 1394.762 8.997 3.737 1382.029 1 BioPieces::Stream#each
1120.951 1.524 1119.426 0.000 79347/79347 IO#eof?
194.922 1.404 0.000 193.519 79346/79346 BioPieces::Filesys#puts
33.544 6.040 0.593 26.911 79346/79346 BioPieces::Stream#read
11.779 7.676 1.286 2.817 79346/79346 BioPieces::Seq#to_fastq
9.993 3.372 0.736 5.886 79346/79346 <Class::BioPieces::Seq>#new_bp
7.930 4.283 1.371 2.276 79346/79346 BioPieces::Seq#qual_convert!
2.909 1.743 0.706 0.460 79346/79346 BioPieces::Seq#length
--------------------------------------------------------------------------------
1120.951 1.524 1119.426 0.000 79347/79347 BioPieces::Stream#each
80.35% 0.11% 1120.951 1.524 1119.426 0.000 79347 IO#eof?
--------------------------------------------------------------------------------
194.922 1.404 0.000 193.519 79346/79346 BioPieces::Stream#each
13.97% 0.10% 194.922 1.404 0.000 193.519 79346 BioPieces::Filesys#puts
193.519 1.090 0.240 192.188 79346/79346 IO#puts
--------------------------------------------------------------------------------
193.519 1.090 0.240 192.188 79346/79346 BioPieces::Filesys#puts
13.87% 0.08% 193.519 1.090 0.240 192.188 79346 IO#puts
192.188 1.161 191.027 0.000 79346/79348 IO#write
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/79348 <Module::Marshal>#dump
192.188 1.161 191.027 0.000 79346/79348 IO#puts
13.78% 0.08% 192.188 1.161 191.027 0.000 79348 IO#write
--------------------------------------------------------------------------------
33.544 6.040 0.593 26.911 79346/79346 BioPieces::Stream#each
2.40% 0.43% 33.544 6.040 0.593 26.911 79346 BioPieces::Stream#read
17.353 2.665 14.688 0.000 158692/158692 IO#read
8.367 4.668 1.771 1.928 79346/79346 <Module::MessagePack>#unpack
0.691 0.691 0.000 0.000 79346/79346 String#unpack
0.501 0.501 0.000 0.000 79346/79346 Array#first
--------------------------------------------------------------------------------
17.353 2.665 14.688 0.000 158692/158692 BioPieces::Stream#read
1.24% 0.19% 17.353 2.665 14.688 0.000 158692 IO#read
--------------------------------------------------------------------------------
11.779 7.676 1.286 2.817 79346/79346 BioPieces::Stream#each
0.84% 0.55% 11.779 7.676 1.286 2.817 79346 BioPieces::Seq#to_fastq
1.425 1.425 0.000 0.000 238038/238038 String#to_s
1.392 1.392 0.000 0.000 238038/317384 Kernel#nil?
--------------------------------------------------------------------------------
9.993 3.372 0.736 5.886 79346/79346 BioPieces::Stream#each
0.72% 0.24% 9.993 3.372 0.736 5.886 79346 <Class::BioPieces::Seq>#new_bp
5.886 1.267 0.147 4.472 79346/79347 Class#new
--------------------------------------------------------------------------------
8.367 4.668 1.771 1.928 79346/79346 BioPieces::Stream#read
0.60% 0.33% 8.367 4.668 1.771 1.928 79346 <Module::MessagePack>#unpack
1.928 1.928 0.000 0.000 317384/317450 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
7.930 4.283 1.371 2.276 79346/79346 BioPieces::Stream#each
0.57% 0.31% 7.930 4.283 1.371 2.276 79346 BioPieces::Seq#qual_convert!
2.276 2.276 0.000 0.000 396730/396766 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/79347 <Class::BioPieces::Filesys>#open
5.886 1.267 0.147 4.472 79346/79347 <Class::BioPieces::Seq>#new_bp
0.42% 0.09% 5.886 1.267 0.147 4.472 79347 Class#new
4.472 3.039 1.433 0.000 79346/79346 BioPieces::Seq#initialize
0.000 0.000 0.000 0.000 1/1 BioPieces::Filesys#initialize
--------------------------------------------------------------------------------
4.472 3.039 1.433 0.000 79346/79346 Class#new
0.32% 0.22% 4.472 3.039 1.433 0.000 79346 BioPieces::Seq#initialize
--------------------------------------------------------------------------------
2.909 1.743 0.706 0.460 79346/79346 BioPieces::Stream#each
0.21% 0.12% 2.909 1.743 0.706 0.460 79346 BioPieces::Seq#length
0.460 0.460 0.000 0.000 79346/317384 Kernel#nil?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 36/396766 Hash#each
2.276 2.276 0.000 0.000 396730/396766 BioPieces::Seq#qual_convert!
0.16% 0.16% 2.276 2.276 0.000 0.000 396766 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/317450 String#===
0.000 0.000 0.000 0.000 7/317450 Kernel#respond_to?
0.000 0.000 0.000 0.000 58/317450 <Module::Marshal>#dump
1.928 1.928 0.000 0.000 317384/317450 <Module::MessagePack>#unpack
0.14% 0.14% 1.929 1.929 0.000 0.000 317450 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.460 0.460 0.000 0.000 79346/317384 BioPieces::Seq#length
1.392 1.392 0.000 0.000 238038/317384 BioPieces::Seq#to_fastq
0.13% 0.13% 1.852 1.852 0.000 0.000 317384 Kernel#nil?
--------------------------------------------------------------------------------
1.425 1.425 0.000 0.000 238038/238038 BioPieces::Seq#to_fastq
0.10% 0.10% 1.425 1.425 0.000 0.000 238038 String#to_s
--------------------------------------------------------------------------------
0.691 0.691 0.000 0.000 79346/79346 BioPieces::Stream#read
0.05% 0.05% 0.691 0.691 0.000 0.000 79346 String#unpack
--------------------------------------------------------------------------------
0.501 0.501 0.000 0.000 79346/79346 BioPieces::Stream#read
0.04% 0.04% 0.501 0.501 0.000 0.000 79346 Array#first
--------------------------------------------------------------------------------
0.005 0.000 0.000 0.005 2/3 BioPieces::StatusHelper#status_save
0.065 0.000 0.000 0.065 1/3 <Class::BioPieces::Filesys>#open
0.01% 0.00% 0.071 0.000 0.000 0.070 3 <Class::IO>#open
0.070 0.000 0.065 0.005 3/5 File#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/5 Delegator#method_missing
0.070 0.000 0.065 0.005 3/5 <Class::IO>#open
0.01% 0.00% 0.070 0.000 0.065 0.005 5 *File#initialize
0.003 0.000 0.000 0.002 2/2 Delegator#method_missing
0.002 0.001 0.000 0.001 2/36 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 2/4 IO#close
0.000 0.000 0.000 0.000 2/2 File#to_path
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.005 0.000 0.000 0.005 1/2 Proc#call
0.005 0.000 0.000 0.005 1/2 BioPieces::StatusHelper#status_track
0.00% 0.00% 0.010 0.000 0.000 0.010 2 BioPieces::StatusHelper#status_save
0.005 0.000 0.000 0.005 2/3 <Class::IO>#open
0.005 0.001 0.000 0.003 2/2 Hash#each
0.000 0.000 0.000 0.000 1/1 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.001 2/36 File#initialize
0.003 0.002 0.000 0.001 34/36 Hash#each
0.00% 0.00% 0.005 0.003 0.000 0.002 36 <Module::Marshal>#dump
0.001 0.001 0.000 0.001 6/6 Time#_dump
0.000 0.000 0.000 0.000 58/317450 Kernel#respond_to_missing?
0.000 0.000 0.000 0.000 2/79348 IO#write
0.000 0.000 0.000 0.000 2/2 IO#binmode
--------------------------------------------------------------------------------
0.005 0.001 0.000 0.003 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.005 0.001 0.000 0.003 2 Hash#each
0.003 0.002 0.000 0.001 34/36 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 36/396766 Symbol#==
--------------------------------------------------------------------------------
0.003 0.000 0.000 0.002 2/2 File#initialize
0.00% 0.00% 0.003 0.000 0.000 0.002 2 Delegator#method_missing
0.002 0.000 0.000 0.001 2/2 BasicObject#method_missing
0.000 0.000 0.000 0.000 2/2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
0.000 0.000 0.000 0.000 2/5 File#initialize
--------------------------------------------------------------------------------
0.002 0.000 0.000 0.001 2/2 Delegator#method_missing
0.00% 0.00% 0.002 0.000 0.000 0.001 2 BasicObject#method_missing
0.001 0.000 0.000 0.000 2/2 Array#delete_if
0.000 0.000 0.000 0.000 2/2 NoMethodError#initialize
0.000 0.000 0.000 0.000 6/6 Exception#backtrace
0.000 0.000 0.000 0.000 2/2 Exception#exception
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.001 6/6 <Module::Marshal>#dump
0.00% 0.00% 0.001 0.001 0.000 0.001 6 Time#_dump
0.000 0.000 0.000 0.000 20/20 Fixnum#divmod
0.000 0.000 0.000 0.000 12/12 Fixnum#<=>
0.000 0.000 0.000 0.000 6/6 Fixnum#==
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.001 0.000 0.000 0.000 2 Array#delete_if
0.000 0.000 0.000 0.000 15/15 Regexp#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/4 BioPieces::Stream#close
0.000 0.000 0.000 0.000 1/4 <Class::BioPieces::Filesys>#open
0.000 0.000 0.000 0.000 2/4 File#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 4 IO#close
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NoMethodError#initialize
0.000 0.000 0.000 0.000 2/2 NameError#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Exception#backtrace
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/8 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 2/8 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 8 Kernel#respond_to?
0.000 0.000 0.000 0.000 7/317450 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NoMethodError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NameError#initialize
0.000 0.000 0.000 0.000 2/2 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 15/15 Array#delete_if
0.00% 0.00% 0.000 0.000 0.000 0.000 15 Regexp#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 20/20 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 20 Fixnum#divmod
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NameError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/6 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/6 File#initialize
0.000 0.000 0.000 0.000 2/6 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::Pipeline::Command#run
0.000 0.000 0.000 0.000 1/2 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 2 <Class::Time>#now
0.000 0.000 0.000 0.000 2/2 Time#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/12 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 12 Fixnum#<=>
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 <Class::BioPieces::Filesys>#open
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Kernel#block_given?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 4/4 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 4 IO#set_encoding
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Class::Time>#now
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Time#initialize
0.000 0.000 0.000 0.000 2/2 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Fixnum#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 File#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 File#to_path
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Class#new
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Filesys#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.000 0.000 0.000 0.000 1 BioPieces::Stream#close
0.000 0.000 0.000 0.000 1/4 IO#close
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Module#include
0.000 0.000 0.000 0.000 1/1 Module#append_features
0.000 0.000 0.000 0.000 1/1 Module#included
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 8/8 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 8 Module#method_added
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Module::Marshal>#dump
0.00% 0.00% 0.000 0.000 0.000 0.000 2 IO#binmode
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 String#===
0.000 0.000 0.000 0.000 1/317450 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#exception
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 4/4 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 4 Class#inherited
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Time#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 3 BasicObject#singleton_method_added
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 <Class::BioPieces::Filesys>#open
0.00% 0.00% 0.000 0.000 0.000 0.000 3 Array#shift
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 3/3 <Class::BioPieces::Filesys>#open
0.00% 0.00% 0.000 0.000 0.000 0.000 3 Symbol#===
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Module#include
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Module#append_features
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Module#include
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Module#included
* indicates recursively called methods
Thread ID: 70106804478460
Fiber ID: 70106778482180
Total Time: 1395.1102439
Sort by: total_time
%total %self total self wait child calls Name
--------------------------------------------------------------------------------
100.00% 0.00% 1395.110 0.000 0.000 1395.110 1 BioPieces::Pipeline#run_thread
1395.110 0.000 0.000 1395.110 1/1 BioPieces::Pipeline::Command#run
--------------------------------------------------------------------------------
1395.110 0.000 0.000 1395.110 1/1 BioPieces::Pipeline#run_thread
100.00% 0.00% 1395.110 0.000 0.000 1395.110 1 BioPieces::Pipeline::Command#run
1395.110 0.000 0.378 1394.732 1/2 Proc#call
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::StatusHelper#status_track
1395.110 0.000 0.378 1394.732 1/2 BioPieces::Pipeline::Command#run
100.00% 0.00% 1395.110 0.000 0.378 1394.732 2 *Proc#call
1394.716 0.000 0.000 1394.716 1/1 BioPieces::StatusHelper#status_track
1394.617 56.359 13.493 1324.765 1/1 BioPieces::Stream#each
0.016 0.000 0.000 0.016 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
0.000 0.000 0.000 0.000 1/1 Symbol#to_sym
0.000 0.000 0.000 0.000 2/2 Fixnum#to_f
0.000 0.000 0.000 0.000 2/2 Float#/
0.000 0.000 0.000 0.000 1/1 Fixnum#*
--------------------------------------------------------------------------------
1394.716 0.000 0.000 1394.716 1/1 Proc#call
99.97% 0.00% 1394.716 0.000 0.000 1394.716 1 BioPieces::StatusHelper#status_track
0.098 0.000 0.000 0.098 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/2 Proc#call
--------------------------------------------------------------------------------
1394.617 56.359 13.493 1324.765 1/1 Proc#call
99.96% 4.04% 1394.617 56.359 13.493 1324.765 1 BioPieces::Stream#each
696.568 31.075 0.000 665.494 370638/370638 BioPieces::Stream#write
279.944 24.488 2.840 252.616 370638/370638 BioPieces::Stream#read
172.183 12.265 0.133 159.785 370638/370638 BioPieces::Trim#quality_trim!
89.474 4.390 85.083 0.000 370639/370639 IO#eof?
42.978 15.462 2.750 24.766 370638/370638 <Class::BioPieces::Seq>#new_bp
24.670 16.166 4.210 4.294 741276/1482552 BioPieces::Seq#length
15.731 15.731 0.000 0.000 370638/370638 BioPieces::Seq#to_bp
3.217 3.217 0.000 0.000 370638/370638 Hash#merge!
--------------------------------------------------------------------------------
696.568 31.075 0.000 665.494 370638/370638 BioPieces::Stream#each
49.93% 2.23% 696.568 31.075 0.000 665.494 370638 BioPieces::Stream#write
631.054 25.719 605.334 0.000 741276/741278 IO#write
30.627 16.109 5.994 8.525 370638/370638 <Module::MessagePack>#pack
3.812 3.812 0.000 0.000 370638/370638 Array#pack
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/741278 <Module::Marshal>#dump
631.054 25.719 605.334 0.000 741276/741278 BioPieces::Stream#write
45.23% 1.84% 631.054 25.720 605.334 0.000 741278 IO#write
--------------------------------------------------------------------------------
279.944 24.488 2.840 252.616 370638/370638 BioPieces::Stream#each
20.07% 1.76% 279.944 24.488 2.840 252.616 370638 BioPieces::Stream#read
208.141 9.959 198.181 0.000 741276/741276 IO#read
39.109 21.114 9.287 8.708 370638/370638 <Module::MessagePack>#unpack
3.113 3.113 0.000 0.000 370638/370638 String#unpack
2.253 2.253 0.000 0.000 370638/370638 Array#first
--------------------------------------------------------------------------------
208.141 9.959 198.181 0.000 741276/741276 BioPieces::Stream#read
14.92% 0.71% 208.141 9.959 198.181 0.000 741276 IO#read
--------------------------------------------------------------------------------
172.183 12.265 0.133 159.785 370638/370638 BioPieces::Stream#each
12.34% 0.88% 172.183 12.265 0.133 159.785 370638 BioPieces::Trim#quality_trim!
159.785 25.224 8.070 126.492 370638/370638 BioPieces::Trim#quality_trim
--------------------------------------------------------------------------------
159.785 25.224 8.070 126.492 370638/370638 BioPieces::Trim#quality_trim!
11.45% 1.81% 159.785 25.224 8.070 126.492 370638 BioPieces::Trim#quality_trim
54.750 22.799 0.000 31.951 370638/370638 BioPieces::Seq#[]
41.781 18.521 5.603 17.657 370638/370638 BioPieces::Trim#check_trim_args
24.740 15.913 4.718 4.109 741276/1482552 BioPieces::Seq#length
2.822 2.822 0.000 0.000 370638/370638 BioPieces::Trim#trim_right_pos_c
2.398 2.398 0.000 0.000 370638/370638 BioPieces::Trim#trim_left_pos_c
--------------------------------------------------------------------------------
89.474 4.390 85.083 0.000 370639/370639 BioPieces::Stream#each
6.41% 0.31% 89.474 4.390 85.083 0.000 370639 IO#eof?
--------------------------------------------------------------------------------
54.750 22.799 0.000 31.951 370638/370638 BioPieces::Trim#quality_trim
3.92% 1.63% 54.750 22.799 0.000 31.951 370638 BioPieces::Seq#[]
22.828 5.071 0.237 17.521 370638/741276 Class#new
6.913 6.913 0.000 0.000 741276/741276 String#[]
2.210 2.210 0.000 0.000 370638/2594466 Kernel#nil?
--------------------------------------------------------------------------------
24.670 16.166 4.210 4.294 741276/1482552 BioPieces::Stream#each
24.740 15.913 4.718 4.109 741276/1482552 BioPieces::Trim#quality_trim
3.54% 2.30% 49.410 32.080 8.928 8.402 1482552 BioPieces::Seq#length
8.402 8.402 0.000 0.000 1482552/2594466 Kernel#nil?
--------------------------------------------------------------------------------
22.828 5.071 0.237 17.521 370638/741276 BioPieces::Seq#[]
24.766 5.559 0.272 18.935 370638/741276 <Class::BioPieces::Seq>#new_bp
3.41% 0.76% 47.595 10.630 0.509 36.456 741276 Class#new
36.456 26.820 9.636 0.000 741276/741276 BioPieces::Seq#initialize
--------------------------------------------------------------------------------
42.978 15.462 2.750 24.766 370638/370638 BioPieces::Stream#each
3.08% 1.11% 42.978 15.462 2.750 24.766 370638 <Class::BioPieces::Seq>#new_bp
24.766 5.559 0.272 18.935 370638/741276 Class#new
--------------------------------------------------------------------------------
41.781 18.521 5.603 17.657 370638/370638 BioPieces::Trim#quality_trim
2.99% 1.33% 41.781 18.521 5.603 17.657 370638 BioPieces::Trim#check_trim_args
13.480 6.543 2.608 4.329 370638/370638 Range#include?
4.176 4.176 0.000 0.000 741276/2594466 Kernel#nil?
--------------------------------------------------------------------------------
39.109 21.114 9.287 8.708 370638/370638 BioPieces::Stream#read
2.80% 1.51% 39.109 21.114 9.287 8.708 370638 <Module::MessagePack>#unpack
8.708 8.708 0.000 0.000 1482552/2965160 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
36.456 26.820 9.636 0.000 741276/741276 Class#new
2.61% 1.92% 36.456 26.820 9.636 0.000 741276 BioPieces::Seq#initialize
--------------------------------------------------------------------------------
30.627 16.109 5.994 8.525 370638/370638 BioPieces::Stream#write
2.20% 1.15% 30.627 16.109 5.994 8.525 370638 <Module::MessagePack>#pack
8.525 8.525 0.000 0.000 1482552/2965160 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/2965160 Kernel#respond_to?
0.000 0.000 0.000 0.000 50/2965160 <Module::Marshal>#dump
8.525 8.525 0.000 0.000 1482552/2965160 <Module::MessagePack>#pack
8.708 8.708 0.000 0.000 1482552/2965160 <Module::MessagePack>#unpack
1.24% 1.24% 17.233 17.233 0.000 0.000 2965160 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
15.731 15.731 0.000 0.000 370638/370638 BioPieces::Stream#each
1.13% 1.13% 15.731 15.731 0.000 0.000 370638 BioPieces::Seq#to_bp
--------------------------------------------------------------------------------
2.210 2.210 0.000 0.000 370638/2594466 BioPieces::Seq#[]
4.176 4.176 0.000 0.000 741276/2594466 BioPieces::Trim#check_trim_args
8.402 8.402 0.000 0.000 1482552/2594466 BioPieces::Seq#length
1.06% 1.06% 14.789 14.789 0.000 0.000 2594466 Kernel#nil?
--------------------------------------------------------------------------------
13.480 6.543 2.608 4.329 370638/370638 BioPieces::Trim#check_trim_args
0.97% 0.47% 13.480 6.543 2.608 4.329 370638 Range#include?
4.329 4.329 0.000 0.000 741276/741288 Fixnum#<=>
--------------------------------------------------------------------------------
6.913 6.913 0.000 0.000 741276/741276 BioPieces::Seq#[]
0.50% 0.50% 6.913 6.913 0.000 0.000 741276 String#[]
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/741288 Time#_dump
4.329 4.329 0.000 0.000 741276/741288 Range#include?
0.31% 0.31% 4.329 4.329 0.000 0.000 741288 Fixnum#<=>
--------------------------------------------------------------------------------
3.812 3.812 0.000 0.000 370638/370638 BioPieces::Stream#write
0.27% 0.27% 3.812 3.812 0.000 0.000 370638 Array#pack
--------------------------------------------------------------------------------
3.217 3.217 0.000 0.000 370638/370638 BioPieces::Stream#each
0.23% 0.23% 3.217 3.217 0.000 0.000 370638 Hash#merge!
--------------------------------------------------------------------------------
3.113 3.113 0.000 0.000 370638/370638 BioPieces::Stream#read
0.22% 0.22% 3.113 3.113 0.000 0.000 370638 String#unpack
--------------------------------------------------------------------------------
2.822 2.822 0.000 0.000 370638/370638 BioPieces::Trim#quality_trim
0.20% 0.20% 2.822 2.822 0.000 0.000 370638 BioPieces::Trim#trim_right_pos_c
--------------------------------------------------------------------------------
2.398 2.398 0.000 0.000 370638/370638 BioPieces::Trim#quality_trim
0.17% 0.17% 2.398 2.398 0.000 0.000 370638 BioPieces::Trim#trim_left_pos_c
--------------------------------------------------------------------------------
2.253 2.253 0.000 0.000 370638/370638 BioPieces::Stream#read
0.16% 0.16% 2.253 2.253 0.000 0.000 370638 Array#first
--------------------------------------------------------------------------------
0.016 0.000 0.000 0.016 1/2 Proc#call
0.098 0.000 0.000 0.098 1/2 BioPieces::StatusHelper#status_track
0.01% 0.00% 0.114 0.000 0.000 0.114 2 BioPieces::StatusHelper#status_save
0.099 0.000 0.000 0.099 2/2 <Class::IO>#open
0.014 0.002 0.000 0.012 2/2 Hash#each
0.000 0.000 0.000 0.000 2/2 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
--------------------------------------------------------------------------------
0.099 0.000 0.000 0.099 2/2 BioPieces::StatusHelper#status_save
0.01% 0.00% 0.099 0.000 0.000 0.099 2 <Class::IO>#open
0.099 0.000 0.000 0.099 2/4 File#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/4 Delegator#method_missing
0.099 0.000 0.000 0.099 2/4 <Class::IO>#open
0.01% 0.00% 0.099 0.000 0.000 0.099 4 *File#initialize
0.078 0.000 0.078 0.000 2/4 IO#close
0.019 0.001 0.016 0.002 2/2 Delegator#method_missing
0.002 0.001 0.000 0.001 2/56 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
0.000 0.000 0.000 0.000 2/2 File#to_path
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/4 BioPieces::Stream#close
0.078 0.000 0.078 0.000 2/4 File#initialize
0.01% 0.00% 0.079 0.000 0.078 0.000 4 IO#close
--------------------------------------------------------------------------------
0.019 0.001 0.016 0.002 2/2 File#initialize
0.00% 0.00% 0.019 0.001 0.016 0.002 2 Delegator#method_missing
0.001 0.000 0.000 0.001 2/2 BasicObject#method_missing
0.000 0.000 0.000 0.000 2/2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
0.000 0.000 0.000 0.000 2/4 File#initialize
--------------------------------------------------------------------------------
0.014 0.002 0.000 0.012 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.014 0.002 0.000 0.012 2 Hash#each
0.012 0.002 0.008 0.001 54/56 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 56/56 Symbol#==
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.001 2/56 File#initialize
0.012 0.002 0.008 0.001 54/56 Hash#each
0.00% 0.00% 0.014 0.003 0.008 0.002 56 <Module::Marshal>#dump
0.001 0.001 0.000 0.000 6/6 Time#_dump
0.000 0.000 0.000 0.000 50/2965160 Kernel#respond_to_missing?
0.000 0.000 0.000 0.000 2/741278 IO#write
0.000 0.000 0.000 0.000 2/2 IO#binmode
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.001 2/2 Delegator#method_missing
0.00% 0.00% 0.001 0.000 0.000 0.001 2 BasicObject#method_missing
0.001 0.000 0.000 0.000 2/2 Array#delete_if
0.000 0.000 0.000 0.000 6/6 Exception#backtrace
0.000 0.000 0.000 0.000 2/2 NoMethodError#initialize
0.000 0.000 0.000 0.000 2/2 Exception#exception
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.000 6/6 <Module::Marshal>#dump
0.00% 0.00% 0.001 0.001 0.000 0.000 6 Time#_dump
0.000 0.000 0.000 0.000 20/20 Fixnum#divmod
0.000 0.000 0.000 0.000 12/741288 Fixnum#<=>
0.000 0.000 0.000 0.000 6/6 Fixnum#==
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.001 0.000 0.000 0.000 2 Array#delete_if
0.000 0.000 0.000 0.000 15/15 Regexp#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 56/56 Hash#each
0.00% 0.00% 0.000 0.000 0.000 0.000 56 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 15/15 Array#delete_if
0.00% 0.00% 0.000 0.000 0.000 0.000 15 Regexp#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 Proc#call
0.000 0.000 0.000 0.000 1/2 BioPieces::Pipeline::Command#run
0.00% 0.00% 0.000 0.000 0.000 0.000 2 <Class::Time>#now
0.000 0.000 0.000 0.000 2/2 Time#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/8 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 2/8 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 8 Kernel#respond_to?
0.000 0.000 0.000 0.000 6/2965160 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Exception#backtrace
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 20/20 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 20 Fixnum#divmod
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NoMethodError#initialize
0.000 0.000 0.000 0.000 2/2 NameError#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Class::Time>#now
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Time#initialize
0.000 0.000 0.000 0.000 2/2 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/6 File#initialize
0.000 0.000 0.000 0.000 2/6 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/6 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.000 0.000 0.000 0.000 2 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/4 IO#close
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NoMethodError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NameError#initialize
0.000 0.000 0.000 0.000 2/2 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Fixnum#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Time#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NameError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Symbol#to_sym
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Module::Marshal>#dump
0.00% 0.00% 0.000 0.000 0.000 0.000 2 IO#binmode
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 File#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 File#to_path
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Fixnum#to_f
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#exception
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Float#/
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/1 Proc#call
0.00% 0.00% 0.000 0.000 0.000 0.000 1 Fixnum#*
* indicates recursively called methods
Thread ID: 70106804478720
Fiber ID: 70106778481860
Total Time: 1395.109011904
Sort by: total_time
%total %self total self wait child calls Name
--------------------------------------------------------------------------------
100.00% 0.00% 1395.109 0.000 0.000 1395.109 1 BioPieces::Pipeline#run_thread
1395.109 0.000 0.000 1395.109 1/1 BioPieces::Pipeline::Command#run
--------------------------------------------------------------------------------
1395.109 0.000 0.000 1395.109 1/1 BioPieces::Pipeline#run_thread
100.00% 0.00% 1395.109 0.000 0.000 1395.109 1 BioPieces::Pipeline::Command#run
1395.108 0.000 0.369 1394.739 1/2 Proc#call
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 BioPieces::StatusHelper#status_track
1395.108 0.000 0.369 1394.739 1/2 BioPieces::Pipeline::Command#run
100.00% 0.00% 1395.108 0.000 0.369 1394.739 2 *Proc#call
1394.735 0.000 0.000 1394.735 1/1 BioPieces::StatusHelper#status_track
1394.731 40.839 7.923 1345.968 1/1 BioPieces::Stream#each
0.004 0.000 0.000 0.004 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/2 <Class::Time>#now
--------------------------------------------------------------------------------
1394.735 0.000 0.000 1394.735 1/1 Proc#call
99.97% 0.00% 1394.735 0.000 0.000 1394.735 1 BioPieces::StatusHelper#status_track
0.004 0.000 0.000 0.004 1/2 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 1/2 Proc#call
--------------------------------------------------------------------------------
1394.731 40.839 7.923 1345.968 1/1 Proc#call
99.97% 2.93% 1394.731 40.839 7.923 1345.968 1 BioPieces::Stream#each
602.466 31.422 0.000 571.044 370638/370638 BioPieces::Stream#write
376.112 4.587 371.526 0.000 370639/370639 IO#eof?
190.803 25.015 4.322 161.466 370638/370638 BioPieces::Stream#read
130.261 19.107 3.661 107.493 370503/370503 BioPieces::Seq#scores_mean
43.206 15.741 3.335 24.130 370503/370503 <Class::BioPieces::Seq>#new_bp
3.120 3.120 0.000 0.000 370503/370503 Float#round
--------------------------------------------------------------------------------
602.466 31.422 0.000 571.044 370638/370638 BioPieces::Stream#each
43.18% 2.25% 602.466 31.422 0.000 571.044 370638 BioPieces::Stream#write
536.868 24.913 511.955 0.000 741276/741278 IO#write
30.409 16.600 5.033 8.776 370638/370638 <Module::MessagePack>#pack
3.767 3.767 0.000 0.000 370638/370638 Array#pack
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/741278 <Module::Marshal>#dump
536.868 24.913 511.955 0.000 741276/741278 BioPieces::Stream#write
38.48% 1.79% 536.868 24.913 511.955 0.000 741278 IO#write
--------------------------------------------------------------------------------
376.112 4.587 371.526 0.000 370639/370639 BioPieces::Stream#each
26.96% 0.33% 376.112 4.587 371.526 0.000 370639 IO#eof?
--------------------------------------------------------------------------------
190.803 25.015 4.322 161.466 370638/370638 BioPieces::Stream#each
13.68% 1.79% 190.803 25.015 4.322 161.466 370638 BioPieces::Stream#read
115.707 10.110 105.597 0.000 741276/741276 IO#read
40.456 22.422 9.024 9.010 370638/370638 <Module::MessagePack>#unpack
3.048 3.048 0.000 0.000 370638/370638 String#unpack
2.255 2.255 0.000 0.000 370638/370638 Array#first
--------------------------------------------------------------------------------
130.261 19.107 3.661 107.493 370503/370503 BioPieces::Stream#each
9.34% 1.37% 130.261 19.107 3.661 107.493 370503 BioPieces::Seq#scores_mean
83.375 26.193 5.269 51.913 370503/370503 NArray#mean
17.013 10.479 4.018 2.517 370503/370503 NArray#-
4.775 4.775 0.000 0.000 370503/370503 <Class::NArray>#to_na
2.330 2.330 0.000 0.000 370503/370503 Kernel#nil?
--------------------------------------------------------------------------------
115.707 10.110 105.597 0.000 741276/741276 BioPieces::Stream#read
8.29% 0.72% 115.707 10.110 105.597 0.000 741276 IO#read
--------------------------------------------------------------------------------
83.375 26.193 5.269 51.913 370503/370503 BioPieces::Seq#scores_mean
5.98% 1.88% 83.375 26.193 5.269 51.913 370503 NArray#mean
16.824 8.620 5.892 2.312 370503/370503 NArray#rank_total
13.121 6.485 4.355 2.281 370503/370503 NArray#integer?
8.833 8.833 0.000 0.000 370503/370503 NArray#sum
7.406 7.406 0.000 0.000 370503/370503 NArray#to_type
3.416 3.416 0.000 0.000 370503/370503 <Class::NArray>#ref
2.313 2.313 0.000 0.000 370503/370503 Float#/
--------------------------------------------------------------------------------
43.206 15.741 3.335 24.130 370503/370503 BioPieces::Stream#each
3.10% 1.13% 43.206 15.741 3.335 24.130 370503 <Class::BioPieces::Seq>#new_bp
24.130 5.633 0.185 18.312 370503/370503 Class#new
--------------------------------------------------------------------------------
40.456 22.422 9.024 9.010 370638/370638 BioPieces::Stream#read
2.90% 1.61% 40.456 22.422 9.024 9.010 370638 <Module::MessagePack>#unpack
9.010 9.010 0.000 0.000 1482552/2965160 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
30.409 16.600 5.033 8.776 370638/370638 BioPieces::Stream#write
2.18% 1.19% 30.409 16.600 5.033 8.776 370638 <Module::MessagePack>#pack
8.776 8.776 0.000 0.000 1482552/2965160 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
24.130 5.633 0.185 18.312 370503/370503 <Class::BioPieces::Seq>#new_bp
1.73% 0.40% 24.130 5.633 0.185 18.312 370503 Class#new
18.312 14.023 4.289 0.000 370503/370503 BioPieces::Seq#initialize
--------------------------------------------------------------------------------
18.312 14.023 4.289 0.000 370503/370503 Class#new
1.31% 1.01% 18.312 14.023 4.289 0.000 370503 BioPieces::Seq#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/2965160 Kernel#respond_to?
0.000 0.000 0.000 0.000 50/2965160 <Module::Marshal>#dump
8.776 8.776 0.000 0.000 1482552/2965160 <Module::MessagePack>#pack
9.010 9.010 0.000 0.000 1482552/2965160 <Module::MessagePack>#unpack
1.27% 1.27% 17.786 17.786 0.000 0.000 2965160 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
17.013 10.479 4.018 2.517 370503/370503 BioPieces::Seq#scores_mean
1.22% 0.75% 17.013 10.479 4.018 2.517 370503 NArray#-
2.517 2.517 0.000 0.000 370503/370503 Module#<=
--------------------------------------------------------------------------------
16.824 8.620 5.892 2.312 370503/370503 NArray#mean
1.21% 0.62% 16.824 8.620 5.892 2.312 370503 NArray#rank_total
2.312 2.312 0.000 0.000 370503/370503 NArray#total
--------------------------------------------------------------------------------
13.121 6.485 4.355 2.281 370503/370503 NArray#mean
0.94% 0.46% 13.121 6.485 4.355 2.281 370503 NArray#integer?
2.281 2.281 0.000 0.000 370503/370503 NArray#typecode
--------------------------------------------------------------------------------
8.833 8.833 0.000 0.000 370503/370503 NArray#mean
0.63% 0.63% 8.833 8.833 0.000 0.000 370503 NArray#sum
--------------------------------------------------------------------------------
7.406 7.406 0.000 0.000 370503/370503 NArray#mean
0.53% 0.53% 7.406 7.406 0.000 0.000 370503 NArray#to_type
--------------------------------------------------------------------------------
4.775 4.775 0.000 0.000 370503/370503 BioPieces::Seq#scores_mean
0.34% 0.34% 4.775 4.775 0.000 0.000 370503 <Class::NArray>#to_na
--------------------------------------------------------------------------------
3.767 3.767 0.000 0.000 370638/370638 BioPieces::Stream#write
0.27% 0.27% 3.767 3.767 0.000 0.000 370638 Array#pack
--------------------------------------------------------------------------------
3.416 3.416 0.000 0.000 370503/370503 NArray#mean
0.24% 0.24% 3.416 3.416 0.000 0.000 370503 <Class::NArray>#ref
--------------------------------------------------------------------------------
3.120 3.120 0.000 0.000 370503/370503 BioPieces::Stream#each
0.22% 0.22% 3.120 3.120 0.000 0.000 370503 Float#round
--------------------------------------------------------------------------------
3.048 3.048 0.000 0.000 370638/370638 BioPieces::Stream#read
0.22% 0.22% 3.048 3.048 0.000 0.000 370638 String#unpack
--------------------------------------------------------------------------------
2.517 2.517 0.000 0.000 370503/370503 NArray#-
0.18% 0.18% 2.517 2.517 0.000 0.000 370503 Module#<=
--------------------------------------------------------------------------------
2.330 2.330 0.000 0.000 370503/370503 BioPieces::Seq#scores_mean
0.17% 0.17% 2.330 2.330 0.000 0.000 370503 Kernel#nil?
--------------------------------------------------------------------------------
2.313 2.313 0.000 0.000 370503/370503 NArray#mean
0.17% 0.17% 2.313 2.313 0.000 0.000 370503 Float#/
--------------------------------------------------------------------------------
2.312 2.312 0.000 0.000 370503/370503 NArray#rank_total
0.17% 0.17% 2.312 2.312 0.000 0.000 370503 NArray#total
--------------------------------------------------------------------------------
2.281 2.281 0.000 0.000 370503/370503 NArray#integer?
0.16% 0.16% 2.281 2.281 0.000 0.000 370503 NArray#typecode
--------------------------------------------------------------------------------
2.255 2.255 0.000 0.000 370638/370638 BioPieces::Stream#read
0.16% 0.16% 2.255 2.255 0.000 0.000 370638 Array#first
--------------------------------------------------------------------------------
0.004 0.000 0.000 0.004 1/2 BioPieces::StatusHelper#status_track
0.004 0.000 0.000 0.004 1/2 Proc#call
0.00% 0.00% 0.008 0.000 0.000 0.008 2 BioPieces::StatusHelper#status_save
0.004 0.000 0.000 0.004 2/2 <Class::IO>#open
0.003 0.001 0.000 0.002 2/2 Hash#each
0.000 0.000 0.000 0.000 2/2 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
--------------------------------------------------------------------------------
0.004 0.000 0.000 0.004 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.004 0.000 0.000 0.004 2 <Class::IO>#open
0.004 0.000 0.000 0.004 2/4 File#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/4 Delegator#method_missing
0.004 0.000 0.000 0.004 2/4 <Class::IO>#open
0.00% 0.00% 0.004 0.000 0.000 0.004 4 *File#initialize
0.002 0.001 0.000 0.002 2/2 Delegator#method_missing
0.002 0.001 0.000 0.001 2/28 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 2/4 IO#close
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
0.000 0.000 0.000 0.000 2/2 File#to_path
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.001 2/28 File#initialize
0.002 0.001 0.000 0.001 26/28 Hash#each
0.00% 0.00% 0.004 0.002 0.000 0.002 28 <Module::Marshal>#dump
0.001 0.001 0.000 0.000 6/6 Time#_dump
0.000 0.000 0.000 0.000 50/2965160 Kernel#respond_to_missing?
0.000 0.000 0.000 0.000 2/741278 IO#write
0.000 0.000 0.000 0.000 2/2 IO#binmode
--------------------------------------------------------------------------------
0.003 0.001 0.000 0.002 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.003 0.001 0.000 0.002 2 Hash#each
0.002 0.001 0.000 0.001 26/28 <Module::Marshal>#dump
0.000 0.000 0.000 0.000 28/28 Symbol#==
--------------------------------------------------------------------------------
0.002 0.001 0.000 0.002 2/2 File#initialize
0.00% 0.00% 0.002 0.001 0.000 0.002 2 Delegator#method_missing
0.001 0.000 0.000 0.001 2/2 BasicObject#method_missing
0.000 0.000 0.000 0.000 2/2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
0.000 0.000 0.000 0.000 2/4 File#initialize
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.001 2/2 Delegator#method_missing
0.00% 0.00% 0.001 0.000 0.000 0.001 2 BasicObject#method_missing
0.001 0.000 0.000 0.000 2/2 Array#delete_if
0.000 0.000 0.000 0.000 6/6 Exception#backtrace
0.000 0.000 0.000 0.000 2/2 NoMethodError#initialize
0.000 0.000 0.000 0.000 2/2 Exception#exception
--------------------------------------------------------------------------------
0.001 0.001 0.000 0.000 6/6 <Module::Marshal>#dump
0.00% 0.00% 0.001 0.001 0.000 0.000 6 Time#_dump
0.000 0.000 0.000 0.000 20/20 Fixnum#divmod
0.000 0.000 0.000 0.000 12/12 Fixnum#<=>
0.000 0.000 0.000 0.000 6/6 Fixnum#==
--------------------------------------------------------------------------------
0.001 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.001 0.000 0.000 0.000 2 Array#delete_if
0.000 0.000 0.000 0.000 15/15 Regexp#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/4 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/4 File#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 4 IO#close
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 1/2 Proc#call
0.000 0.000 0.000 0.000 1/2 BioPieces::Pipeline::Command#run
0.00% 0.00% 0.000 0.000 0.000 0.000 2 <Class::Time>#now
0.000 0.000 0.000 0.000 2/2 Time#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/8 Kernel#respond_to?
0.000 0.000 0.000 0.000 2/6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 15/15 Array#delete_if
0.00% 0.00% 0.000 0.000 0.000 0.000 15 Regexp#=~
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 28/28 Hash#each
0.00% 0.00% 0.000 0.000 0.000 0.000 28 Symbol#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/8 BioPieces::StatusHelper#status_save
0.000 0.000 0.000 0.000 2/8 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 4/8 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 8 Kernel#respond_to?
0.000 0.000 0.000 0.000 6/2965160 Kernel#respond_to_missing?
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Exception#backtrace
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 20/20 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 20 Fixnum#divmod
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Class::Time>#now
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Time#initialize
0.000 0.000 0.000 0.000 2/2 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NoMethodError#initialize
0.000 0.000 0.000 0.000 2/2 NameError#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/6 Delegator#respond_to_missing?
0.000 0.000 0.000 0.000 2/6 File#initialize
0.000 0.000 0.000 0.000 2/6 Delegator#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 6 #<Class:0x007f8605e90f88>#__getobj__
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BioPieces::StatusHelper#status_save
0.00% 0.00% 0.000 0.000 0.000 0.000 2 BioPieces::Stream#close
0.000 0.000 0.000 0.000 2/4 IO#close
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 12/12 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 12 Fixnum#<=>
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NoMethodError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 NameError#initialize
0.000 0.000 0.000 0.000 2/2 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 6/6 Time#_dump
0.00% 0.00% 0.000 0.000 0.000 0.000 6 Fixnum#==
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 Time#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Fixnum#+
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 NameError#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#initialize
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 File#initialize
0.00% 0.00% 0.000 0.000 0.000 0.000 2 File#to_path
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 <Module::Marshal>#dump
0.00% 0.00% 0.000 0.000 0.000 0.000 2 IO#binmode
--------------------------------------------------------------------------------
0.000 0.000 0.000 0.000 2/2 BasicObject#method_missing
0.00% 0.00% 0.000 0.000 0.000 0.000 2 Exception#exception
* indicates recursively called methods
Raw
prof_rbx.txt
===== Thread 1 =====
Total running time: 4878.463615274s
index % time self children called name
----------------------------------------------------------
[1] 100.0 0.00 4878.46 1 Rubinius::Loader#script [1]
0.00 4878.46 1 Rubinius::CodeLoader.load_script [2]
0.00 0.00 1 IO.read
-------------------------------------------------------
0.00 4878.46 1 Rubinius::Loader#script [1]
[2] 100.0 0.00 4878.46 1 Rubinius::CodeLoader.load_script [2]
0.00 4878.46 1 Rubinius::CodeLoader#load_script [3]
-------------------------------------------------------
0.00 4878.46 1 Rubinius::CodeLoader.load_script [2]
[3] 100.0 0.00 4878.46 1 Rubinius::CodeLoader#load_script [3]
0.00 4878.44 1 Rubinius.run_script [4]
0.00 0.02 1 Rubinius::CodeLoader#load_file
-------------------------------------------------------
0.00 4878.46 1 Rubinius::CodeLoader#load_script [3]
[4] 100.0 0.00 4878.44 1 Rubinius.run_script [4]
0.00 4878.44 1 script:/disk/orsted/data/maasha/MartinMortensen/Bioconval/Fastq/test_rbx.rb [5]
-------------------------------------------------------
0.00 4878.44 1 Rubinius.run_script [4]
[5] 100.0 0.00 4878.44 1 script:/disk/orsted/data/maasha/MartinMortensen/Bioconval/Fastq/test_rbx.rb [5]
0.00 4859.21 1 Rubinius::Profiler::Instrumenter#profile [6]
0.00 19.23 1 Kernel#require
-------------------------------------------------------
0.00 4878.44 1 script:/disk/orsted/data/maasha/MartinMortensen/Bioconval/Fastq/test_rbx.rb [5]
[6] 99.6 0.00 4859.21 1 Rubinius::Profiler::Instrumenter#profile [6]
0.00 4858.91 1 Object::__script__<7> {} [7]
0.00 0.29 1 Rubinius::Profiler::Instrumenter#start
0.00 0.00 1 Rubinius::Profiler::Instrumenter#stop
-------------------------------------------------------
0.00 4859.21 1 Rubinius::Profiler::Instrumenter#profile [6]
[7] 99.6 0.00 4858.91 1 Object::__script__<7> {} [7]
0.00 4858.91 1 BioPieces::Pipeline#run [8]
0.00 0.00 1 BioPieces::Commands#read_fastq
-------------------------------------------------------
0.00 4858.91 1 Object::__script__<7> {} [7]
[8] 99.6 0.00 4858.91 1 BioPieces::Pipeline#run [8]
0.00 4858.40 1 BioPieces::Pipeline#run_thread [9]
0.00 0.47 1 BioPieces::LogHelper#log_ok
0.00 0.02 1 BioPieces::StatusHelper#status_load
0.00 0.01 1 BioPieces::HistoryHelper#history_save
0.00 0.01 1 BioPieces::StatusHelper#status_init
-------------------------------------------------------
0.00 4858.91 1 BioPieces::Pipeline#run [8]
[9] 99.6 0.00 4858.40 1 BioPieces::Pipeline#run_thread [9]
0.00 4857.48 1 BioPieces::Pipeline::Command#run [10]
0.00 0.91 2 Array#each
-------------------------------------------------------
0.00 4858.40 1 BioPieces::Pipeline#run_thread [9]
[10] 99.6 0.00 4857.48 1 BioPieces::Pipeline::Command#run [10]
0.00 4857.46 1 Proc#call [11]
0.00 0.02 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4857.48 1 BioPieces::Pipeline::Command#run [10]
[11] 99.6 0.00 4857.46 1 Proc#call [11]
0.00 4857.46 1 BioPieces::Commands::read_fastq<96> {} [12]
-------------------------------------------------------
0.00 4857.46 1 Proc#call [11]
[12] 99.6 0.00 4857.46 1 BioPieces::Commands::read_fastq<96> {} [12]
0.00 4857.46 1 BioPieces::StatusHelper#status_track [13]
-------------------------------------------------------
0.00 4857.46 1 BioPieces::Commands::read_fastq<96> {} [12]
[13] 99.6 0.00 4857.46 1 BioPieces::StatusHelper#status_track [13]
0.00 4857.44 1 Proc#call [14]
0.00 0.02 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4857.46 1 BioPieces::StatusHelper#status_track [13]
[14] 99.6 0.00 4857.44 1 Proc#call [14]
0.00 4857.44 1 BioPieces::Commands::read_fastq<97> {} [15]
-------------------------------------------------------
0.00 4857.44 1 Proc#call [14]
[15] 99.6 0.00 4857.44 1 BioPieces::Commands::read_fastq<97> {} [15]
0.00 4857.44 1 Kernel#catch [16]
-------------------------------------------------------
0.00 4857.44 1 BioPieces::Commands::read_fastq<97> {} [15]
[16] 99.6 0.00 4857.44 1 Kernel#catch [16]
0.00 4857.44 1 Rubinius::ThrownValue.register [17]
-------------------------------------------------------
0.00 4857.44 1 Kernel#catch [16]
[17] 99.6 0.00 4857.44 1 Rubinius::ThrownValue.register [17]
0.00 4857.44 1 Kernel::catch<29> {} [18]
-------------------------------------------------------
0.00 4857.44 1 Rubinius::ThrownValue.register [17]
[18] 99.6 0.00 4857.44 1 Kernel::catch<29> {} [18]
0.00 4857.44 1 Rubinius.catch [19]
-------------------------------------------------------
0.00 4857.44 1 Kernel::catch<29> {} [18]
[19] 99.6 0.00 4857.44 1 Rubinius.catch [19]
0.00 4857.44 1 Proc#call [20]
-------------------------------------------------------
0.00 4857.44 1 Rubinius.catch [19]
[20] 99.6 0.00 4857.44 1 Proc#call [20]
0.00 4857.44 1 BioPieces::Commands::read_fastq<112> {} [21]
-------------------------------------------------------
0.00 4857.44 1 Proc#call [20]
[21] 99.6 0.00 4857.44 1 BioPieces::Commands::read_fastq<112> {} [21]
0.00 4857.44 1 Range#each [22]
-------------------------------------------------------
0.00 4857.44 1 BioPieces::Commands::read_fastq<112> {} [21]
[22] 99.6 0.00 4857.44 1 Range#each [22]
14.78 4842.66 1 BioPieces::Commands::read_fastq<118> {} [23]
-------------------------------------------------------
0.00 4857.44 1 Range#each [22]
[23] 99.6 14.78 4842.66 1 BioPieces::Commands::read_fastq<118> {} [23]
3.62 4035.56 370638 BioPieces::Seq#qual_coerce! [24]
15.66 535.62 370639 BioPieces::Fastq#get_entry [31]
5.84 87.10 370638 BioPieces::Stream#<< [39]
6.76 51.79 370638 BioPieces::Seq#to_bp [44]
5.19 26.51 370638 BioPieces::Seq#qual_convert!
3.18 22.54 370638 BioPieces::Seq#qual_valid?
4.02 16.89 926597 Hash#[]
8.48 4.07 555957 Hash#[]=
2.18 4.68 185319 Comparable#==
2.02 0.29 370638 BioPieces::Seq#length
-------------------------------------------------------
14.78 4842.66 1 BioPieces::Commands::read_fastq<118> {} [23]
[24] 82.8 3.62 4035.56 370638 BioPieces::Seq#qual_coerce! [24]
1.20 4034.06 370638 String#tr! [25]
0.18 0.00 370638 Kernel#nil?
0.11 0.00 370638 Kernel#===
-------------------------------------------------------
3.62 4035.56 370638 BioPieces::Seq#qual_coerce! [24]
[25] 82.7 1.20 4034.06 370638 String#tr! [25]
15.47 4018.58 370638 String#tr_trans [26]
-------------------------------------------------------
1.20 4034.06 370638 String#tr! [25]
[26] 82.7 15.47 4018.58 370638 String#tr_trans [26]
830.42 3163.26 741276 String#each_char [27]
4.00 7.21 1111914 String#dup
1.20 8.45 370638 Hash.new_from_literal
0.85 0.11 370638 String#empty?
0.84 0.00 370638 Rubinius::Tuple.pattern
0.66 0.00 370638 String#[]
0.58 0.00 741276 String#tr_expand!
0.52 0.00 741276 Kernel#StringValue
0.22 0.00 370638 String#size
0.16 0.00 370638 String#==
-------------------------------------------------------
15.47 4018.58 370638 String#tr_trans [26]
[27] 81.9 830.42 3163.26 741276 String#each_char [27]
1082.22 1672.68 93030138 String::tr_trans<2452> {} [28]
183.30 35.65 20385090 String::tr_trans<2401> {} [37]
99.99 0.00 113415228 String#find_character [38]
33.75 0.00 113415228 Fixnum#+
33.19 0.00 114156504 Fixnum#<
22.49 0.00 4392 GC.collect_young
0.01 0.00 5 GC.collect_mature
-------------------------------------------------------
830.42 3163.26 741276 String#each_char [27]
[28] 56.5 1082.22 1672.68 93030138 String::tr_trans<2452> {} [28]
493.97 1017.67 93030138 Hash#[] [29]
40.11 0.00 93030138 Rubinius::Tuple#[]
36.69 0.00 93030138 String#ord
30.13 0.00 93030138 Fixnum#>=
27.00 0.00 93030138 Fixnum#+
26.95 0.00 93030138 Fixnum#==
0.17 0.00 43 GC.collect_young
-------------------------------------------------------
1082.22 1672.68 93030138 String::tr_trans<2452> {} [28]
[29] 31.0 493.97 1017.67 93030138 Hash#[] [29]
629.67 318.93 93030138 Hash#find_item [30]
68.78 0.00 93030138 Hash#default [43]
0.29 0.00 53 GC.collect_young
0.00 0.00 2 GC.collect_mature
-------------------------------------------------------
493.97 1017.67 93030138 Hash#[] [29]
[30] 19.4 629.67 318.93 93030138 Hash#find_item [30]
211.72 27.36 93030138 Hash#key_index [36]
41.59 0.00 93030138 Kernel#hash
38.13 0.00 93030138 Rubinius::Tuple#[]
0.12 0.00 27 GC.collect_young
0.00 0.00 1 GC.collect_mature
-------------------------------------------------------
14.78 4842.66 1 BioPieces::Commands::read_fastq<118> {} [23]
[31] 11.3 15.66 535.62 370639 BioPieces::Fastq#get_entry [31]
10.64 384.75 1482553 IO#gets [32]
41.79 28.51 1111914 String#chomp! [42]
5.69 34.73 370638 BioPieces::Seq#initialize
17.42 9.35 370638 String#[]
2.04 0.23 370638 Range#initialize
0.30 0.00 741276 Class#allocate
0.16 0.00 370638 String#length
0.02 0.00 4 GC.collect_young
-------------------------------------------------------
15.66 535.62 370639 BioPieces::Fastq#get_entry [31]
[32] 8.1 10.64 384.75 1482553 IO#gets [32]
28.98 347.83 1482553 IO#each [33]
6.78 1.17 1482553 Rubinius::GlobalVariables#[]
-------------------------------------------------------
10.64 384.75 1482553 IO#gets [32]
[33] 7.7 28.98 347.83 1482553 IO#each [33]
12.23 316.65 1482553 IO::EachReader#each [34]
9.38 1.33 1482553 IO#ensure_open_and_readable
3.81 0.53 1482553 Module#===
1.79 0.00 1482553 IO::EachReader#initialize
0.63 0.21 1482553 Class#allocate
0.74 0.00 1482553 IO::InternalBuffer#exhausted?
0.53 0.00 1482553 Proc.__from_block__
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
28.98 347.83 1482553 IO#each [33]
[34] 6.7 12.23 316.65 1482553 IO::EachReader#each [34]
49.05 263.11 1482553 IO::EachReader#read_to_separator [35]
3.55 0.44 1482553 String#empty?
0.48 0.00 1482553 Proc.__from_block__
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
12.23 316.65 1482553 IO::EachReader#each [34]
[35] 6.4 49.05 263.11 1482553 IO::EachReader#read_to_separator [35]
5.74 83.07 1482552 IO::gets<1618> {} [40]
15.68 36.16 1482552 IO.read_encode [45]
6.25 35.61 1507619 IO::InternalBuffer#fill_from
5.86 33.45 1507619 IO::InternalBuffer#shift
9.81 4.23 1507619 String#<<
10.26 2.10 1482552 Rubinius::GlobalVariables#[]=
6.73 1.93 1507618 IO::InternalBuffer#find
4.01 0.43 1482552 IO#increment_lineno
0.73 0.00 1507619 IO::InternalBuffer#exhausted?
0.61 0.00 1482552 Kernel#taint
-------------------------------------------------------
629.67 318.93 93030138 Hash#find_item [30]
[36] 4.9 211.72 27.36 93030138 Hash#key_index [36]
27.36 0.00 93030138 Fixnum#&
-------------------------------------------------------
830.42 3163.26 741276 String#each_char [27]
[37] 4.5 183.30 35.65 20385090 String::tr_trans<2401> {} [37]
9.20 0.00 20385090 Rubinius::Tuple#[]=
8.03 0.00 20385090 String#ord
6.21 0.00 20385090 String#[]
5.96 0.00 20385090 Fixnum#<
5.88 0.00 20385090 Fixnum#+
0.22 0.00 741276 Fixnum#>
0.15 0.00 370638 Rubinius::ByteArray#[]
-------------------------------------------------------
830.42 3163.26 741276 String#each_char [27]
[38] 2.0 99.99 0.00 113415228 String#find_character [38]
-------------------------------------------------------
14.78 4842.66 1 BioPieces::Commands::read_fastq<118> {} [23]
[39] 1.9 5.84 87.10 370638 BioPieces::Stream#<< [39]
27.82 18.57 370638 MessagePack.pack
13.54 25.28 741276 IO#write
1.71 0.00 370638 Array#pack
0.19 0.00 370638 String#size
-------------------------------------------------------
49.05 263.11 1482553 IO::EachReader#read_to_separator [35]
[40] 1.8 5.74 83.07 1482552 IO::gets<1618> {} [40]
22.79 60.28 1482552 Rubinius::GlobalVariables#[]= [41]
-------------------------------------------------------
5.74 83.07 1482552 IO::gets<1618> {} [40]
[41] 1.7 22.79 60.28 1482552 Rubinius::GlobalVariables#[]= [41]
27.04 4.84 2965104 Array#[]
6.07 20.41 1482552 Proc#call
1.21 0.00 2965104 Rubinius::LookupTable#[]
0.70 0.00 1482552 Rubinius::LookupTable#key?
0.01 0.00 3 GC.collect_young
-------------------------------------------------------
15.66 535.62 370639 BioPieces::Fastq#get_entry [31]
[42] 1.4 41.79 28.51 1111914 String#chomp! [42]
6.72 7.19 1111914 Rubinius::Mirror.reflect
5.11 0.90 1111914 Rubinius::GlobalVariables#[]
2.17 0.00 2223828 String#chr_at
1.93 0.00 2223828 Rubinius::Mirror::String#previous_byte_index
0.88 0.00 1111914 String#num_bytes=
0.85 0.00 2223828 String#ord
0.63 0.00 2223828 Fixnum#===
0.53 0.00 1111914 Kernel#nil?
0.49 0.00 1111914 String#==
0.46 0.00 1111914 Rubinius::Character#ascii?
-------------------------------------------------------
493.97 1017.67 93030138 Hash#[] [29]
[43] 1.4 68.78 0.00 93030138 Hash#default [43]
-------------------------------------------------------
14.78 4842.66 1 BioPieces::Commands::read_fastq<118> {} [23]
[44] 1.2 6.76 51.79 370638 BioPieces::Seq#to_bp [44]
19.61 22.55 1482552 Hash#[]=
1.10 8.35 370638 Hash.new_from_literal
0.17 0.00 370638 String#length
-------------------------------------------------------
49.05 263.11 1482553 IO::EachReader#read_to_separator [35]
[45] 1.1 15.68 36.16 1482552 IO.read_encode [45]
11.76 9.95 1482552 String#force_encoding
7.58 5.71 1482552 IO#external_encoding
0.70 0.00 1482552 IO#internal_encoding
0.45 0.00 1482552 Kernel#equal?
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
10,200 methods omitted
10,245 methods called a total of 0 times
===== Thread 6 =====
Total running time: 4867.423188213001s
index % time self children called name
----------------------------------------------------------
[1] 100.0 0.00 4867.42 1 Thread#__run__ [1]
0.00 4867.42 1 Proc#call [2]
-------------------------------------------------------
0.00 4867.42 1 Thread#__run__ [1]
[2] 100.0 0.00 4867.42 1 Proc#call [2]
0.00 4867.42 1 Object::__script__<125> {} [3]
-------------------------------------------------------
0.00 4867.42 1 Proc#call [2]
[3] 100.0 0.00 4867.42 1 Object::__script__<125> {} [3]
0.00 4867.42 1 Timeout.watch_channel [4]
-------------------------------------------------------
0.00 4867.42 1 Object::__script__<125> {} [3]
[4] 100.0 0.00 4867.42 1 Timeout.watch_channel [4]
4867.42 0.00 1 Rubinius::Channel#receive [5]
-------------------------------------------------------
0.00 4867.42 1 Timeout.watch_channel [4]
[5] 100.0 4867.42 0.00 1 Rubinius::Channel#receive [5]
-------------------------------------------------------
5 methods called a total of 0 times
===== Thread 7 =====
Total running time: 4858.383629822s
index % time self children called name
----------------------------------------------------------
[1] 100.0 0.00 4858.38 1 Thread#__run__ [1]
0.00 4858.38 1 Proc#call [2]
-------------------------------------------------------
0.00 4858.38 1 Thread#__run__ [1]
[2] 100.0 0.00 4858.38 1 Proc#call [2]
0.00 4858.38 1 BioPieces::Pipeline::run_thread<145> {} [3]
-------------------------------------------------------
0.00 4858.38 1 Proc#call [2]
[3] 100.0 0.00 4858.38 1 BioPieces::Pipeline::run_thread<145> {} [3]
0.00 4858.38 1 BioPieces::Pipeline::Command#run [4]
-------------------------------------------------------
0.00 4858.38 1 BioPieces::Pipeline::run_thread<145> {} [3]
[4] 100.0 0.00 4858.38 1 BioPieces::Pipeline::Command#run [4]
0.00 4858.26 1 Proc#call [5]
0.00 0.12 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4858.38 1 BioPieces::Pipeline::Command#run [4]
[5] 100.0 0.00 4858.26 1 Proc#call [5]
0.00 4858.26 1 BioPieces::Commands::write_fastq<88> {} [6]
-------------------------------------------------------
0.00 4858.26 1 Proc#call [5]
[6] 100.0 0.00 4858.26 1 BioPieces::Commands::write_fastq<88> {} [6]
0.00 4858.26 1 BioPieces::StatusHelper#status_track [7]
-------------------------------------------------------
0.00 4858.26 1 BioPieces::Commands::write_fastq<88> {} [6]
[7] 100.0 0.00 4858.26 1 BioPieces::StatusHelper#status_track [7]
0.00 4858.17 1 Proc#call [8]
0.00 0.08 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4858.26 1 BioPieces::StatusHelper#status_track [7]
[8] 100.0 0.00 4858.17 1 Proc#call [8]
0.00 4858.17 1 BioPieces::Commands::write_fastq<89> {} [9]
-------------------------------------------------------
0.00 4858.17 1 Proc#call [8]
[9] 100.0 0.00 4858.17 1 BioPieces::Commands::write_fastq<89> {} [9]
0.00 4858.15 1 BioPieces::Filesys.open [10]
0.00 0.02 1 Autoload#resolve
-------------------------------------------------------
0.00 4858.17 1 BioPieces::Commands::write_fastq<89> {} [9]
[10] 100.0 0.00 4858.15 1 BioPieces::Filesys.open [10]
0.00 4858.14 1 BioPieces::Commands::write_fastq<122> {} [11]
0.00 0.01 1 IO.open
-------------------------------------------------------
0.00 4858.15 1 BioPieces::Filesys.open [10]
[11] 100.0 0.00 4858.14 1 BioPieces::Commands::write_fastq<122> {} [11]
1.11 4857.02 1 BioPieces::Stream#each [12]
-------------------------------------------------------
0.00 4858.14 1 BioPieces::Commands::write_fastq<122> {} [11]
[12] 100.0 1.11 4857.02 1 BioPieces::Stream#each [12]
0.69 4658.83 79347 IO#eof? [13]
4.34 123.77 79346 BioPieces::Commands::write_fastq<123> {} [18]
2.26 66.81 79346 BioPieces::Stream#read [19]
0.30 0.03 79347 BasicObject#!
-------------------------------------------------------
1.11 4857.02 1 BioPieces::Stream#each [12]
[13] 95.9 0.69 4658.83 79347 IO#eof? [13]
0.41 4657.79 79347 IO::InternalBuffer#fill_from [14]
0.50 0.07 79347 IO#ensure_open_and_readable
0.04 0.00 79348 IO::InternalBuffer#exhausted?
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
0.69 4658.83 79347 IO#eof? [13]
[14] 95.9 0.41 4657.79 79347 IO::InternalBuffer#fill_from [14]
0.83 4656.96 79347 Rubinius.synchronize [15]
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
0.41 4657.79 79347 IO::InternalBuffer#fill_from [14]
[15] 95.9 0.83 4656.96 79347 Rubinius.synchronize [15]
2.09 4654.75 79347 IO::InternalBuffer::fill_from<73> {} [16]
0.08 0.00 79347 Rubinius.unlock
0.04 0.00 79347 Rubinius.lock
-------------------------------------------------------
0.83 4656.96 79347 Rubinius.synchronize [15]
[16] 95.9 2.09 4654.75 79347 IO::InternalBuffer::fill_from<73> {} [16]
4654.01 0.00 79347 IO::InternalBuffer#fill [17]
0.28 0.02 79347 IO::InternalBuffer#size
0.19 0.02 79347 IO::InternalBuffer#empty?
0.11 0.00 79347 IO::InternalBuffer#reset!
0.05 0.00 79347 IO::InternalBuffer#empty_to
0.03 0.00 79347 Fixnum#==
0.03 0.00 79347 Fixnum#<
-------------------------------------------------------
2.09 4654.75 79347 IO::InternalBuffer::fill_from<73> {} [16]
[17] 95.8 4654.01 0.00 79347 IO::InternalBuffer#fill [17]
-------------------------------------------------------
1.11 4857.02 1 BioPieces::Stream#each [12]
[18] 2.6 4.34 123.77 79346 BioPieces::Commands::write_fastq<123> {} [18]
4.25 51.59 79346 BioPieces::Seq#to_fastq [20]
2.37 27.76 79346 BioPieces::Seq.new_bp [23]
0.39 13.26 79346 BioPieces::Filesys#puts [27]
1.70 9.67 476076 Hash#[] [31]
1.12 6.05 79346 BioPieces::Seq#qual_convert! [38]
3.29 1.72 238038 Hash#[]=
0.44 0.07 79346 BioPieces::Seq#length
0.07 0.00 238038 Fixnum#+
0.04 0.00 4 GC.collect_young
-------------------------------------------------------
1.11 4857.02 1 BioPieces::Stream#each [12]
[19] 1.4 2.26 66.81 79346 BioPieces::Stream#read [19]
9.56 26.55 79346 MessagePack.unpack [22]
6.32 17.92 158692 IO#read [25]
0.28 2.53 79346 Hash.new_from_literal
1.33 1.46 79346 Hash#[]=
0.45 0.06 79346 Array#first
0.34 0.00 79346 String#unpack
-------------------------------------------------------
4.34 123.77 79346 BioPieces::Commands::write_fastq<123> {} [18]
[20] 1.1 4.25 51.59 79346 BioPieces::Seq#to_fastq [20]
8.87 40.07 634768 String#+ [21]
1.53 0.27 317384 Rubinius::GlobalVariables#[]
0.58 0.08 238038 String#to_s
0.11 0.00 238038 Kernel#nil?
0.09 0.00 17 GC.collect_young
-------------------------------------------------------
4.25 51.59 79346 BioPieces::Seq#to_fastq [20]
[21] 1.0 8.87 40.07 634768 String#+ [21]
3.18 22.74 634768 String#initialize [24]
4.97 1.27 634768 String.allocate [43]
4.00 1.59 634768 String#<<
1.61 0.26 634768 Rubinius::Type.compatible_encoding
0.42 0.00 634768 Kernel#StringValue
0.04 0.00 8 GC.collect_young
-------------------------------------------------------
2.26 66.81 79346 BioPieces::Stream#read [19]
[22] 0.7 9.56 26.55 79346 MessagePack.unpack [22]
5.80 7.25 396730 Hash#[]= [29]
1.74 4.44 317384 Hash#[] [44]
0.53 3.21 79346 Class#new
0.82 2.72 317384 Kernel#respond_to?
0.03 0.00 79346 Kernel#kind_of?
-------------------------------------------------------
4.34 123.77 79346 BioPieces::Commands::write_fastq<123> {} [18]
[23] 0.6 2.37 27.76 79346 BioPieces::Seq.new_bp [23]
1.59 8.20 79346 BioPieces::Seq#initialize [33]
4.23 4.84 317384 Hash#[]= [35]
1.30 5.78 317384 Hash#[] [39]
0.24 1.54 79346 Hash.new_from_literal
0.04 0.00 79346 Class#allocate
-------------------------------------------------------
8.87 40.07 634768 String#+ [21]
[24] 0.5 3.18 22.74 634768 String#initialize [24]
12.57 9.96 634768 String#replace [26]
0.19 0.00 634768 Kernel#equal?
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
2.26 66.81 79346 BioPieces::Stream#read [19]
[25] 0.5 6.32 17.92 158692 IO#read [25]
0.80 5.59 158692 IO::InternalBuffer#fill_from [41]
0.71 3.82 158692 IO::InternalBuffer#shift
1.30 1.22 158692 String#force_encoding
1.27 0.57 158692 String#<<
1.15 0.16 158692 IO#ensure_open_and_readable
0.45 0.05 158692 BasicObject#!
0.42 0.05 158692 String#empty?
0.15 0.00 317384 IO::InternalBuffer#exhausted?
0.14 0.00 476076 Fixnum#>
0.05 0.00 158692 Fixnum#-
-------------------------------------------------------
3.18 22.74 634768 String#initialize [24]
[26] 0.5 12.57 9.96 634768 String#replace [26]
3.78 4.08 634768 String#force_encoding [36]
0.45 0.00 634768 String#num_bytes=
0.42 0.00 634768 String#shared!
0.42 0.00 634768 Kernel#StringValue
0.21 0.00 634768 String#valid_encoding?
0.20 0.00 634768 Rubinius::Type.object_equal
0.20 0.00 634768 String#encoding
0.20 0.00 634768 Rubinius::Type.infect
0.01 0.00 3 GC.collect_young
-------------------------------------------------------
4.34 123.77 79346 BioPieces::Commands::write_fastq<123> {} [18]
[27] 0.3 0.39 13.26 79346 BioPieces::Filesys#puts [27]
0.59 12.67 79346 IO#puts [28]
-------------------------------------------------------
0.39 13.26 79346 BioPieces::Filesys#puts [27]
[28] 0.3 0.59 12.67 79346 IO#puts [28]
1.03 11.38 79346 Array#each [30]
0.21 0.03 79346 Array#empty?
0.02 0.00 3 GC.collect_young
-------------------------------------------------------
9.56 26.55 79346 MessagePack.unpack [22]
[29] 0.3 5.80 7.25 396730 Hash#[]= [29]
4.14 2.23 396730 Hash#new_bucket [42]
0.22 0.02 79346 Hash::State#match?
0.15 0.00 396730 Rubinius::Tuple#[]
0.14 0.00 396730 Kernel#hash
0.12 0.00 396730 Fixnum#>
0.12 0.00 396730 Fixnum#&
0.11 0.00 317384 Rubinius::Tuple#[]=
-------------------------------------------------------
0.59 12.67 79346 IO#puts [28]
[30] 0.3 1.03 11.38 79346 Array#each [30]
1.34 9.91 79346 IO::puts<1780> {} [32]
0.05 0.00 158692 Fixnum#+
0.05 0.00 158692 Fixnum#<
0.03 0.00 79346 Rubinius::Tuple#at
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
4.34 123.77 79346 BioPieces::Commands::write_fastq<123> {} [18]
[31] 0.2 1.70 9.67 476076 Hash#[] [31]
5.36 4.31 476076 Hash#find_item [34]
-------------------------------------------------------
1.03 11.38 79346 Array#each [30]
[32] 0.2 1.34 9.91 79346 IO::puts<1780> {} [32]
2.91 4.91 79346 IO#write [37]
0.85 0.16 79346 String#suffix?
0.60 0.15 79346 Thread.guarding?
0.20 0.03 79346 String#to_s
0.07 0.00 79346 Kernel#kind_of?
0.02 0.00 79346 Kernel#equal?
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
2.37 27.76 79346 BioPieces::Seq.new_bp [23]
[33] 0.2 1.59 8.20 79346 BioPieces::Seq#initialize [33]
1.06 5.86 317384 Hash#[] [40]
1.04 0.00 158692 String#length
0.22 0.02 79346 BasicObject#!=
-------------------------------------------------------
1.70 9.67 476076 Hash#[] [31]
[34] 0.2 5.36 4.31 476076 Hash#find_item [34]
2.28 0.31 555422 Hash::State#match?
1.21 0.14 476076 Hash#key_index
0.19 0.00 476076 Rubinius::Tuple#[]
0.17 0.00 476076 Kernel#hash
-------------------------------------------------------
2.37 27.76 79346 BioPieces::Seq.new_bp [23]
[35] 0.2 4.23 4.84 317384 Hash#[]= [35]
3.12 1.18 317384 Hash#new_bucket
0.12 0.00 317384 Rubinius::Tuple#[]
0.11 0.00 317384 Rubinius::Tuple#[]=
0.11 0.00 317384 Kernel#hash
0.10 0.00 317384 Fixnum#&
0.09 0.00 317384 Fixnum#>
-------------------------------------------------------
12.57 9.96 634768 String#replace [26]
[36] 0.2 3.78 4.08 634768 String#force_encoding [36]
2.06 1.82 634768 Rubinius::Type.coerce_to_encoding
0.19 0.00 634768 Fixnum#==
-------------------------------------------------------
1.34 9.91 79346 IO::puts<1780> {} [32]
[37] 0.2 2.91 4.91 79346 IO#write [37]
0.38 1.12 79346 IO::InternalBuffer#unseek!
0.52 0.45 79346 IO#binmode?
0.50 0.08 79346 IO#ensure_open_and_writable
0.35 0.05 79343 IO#sync
0.02 0.26 1269 IO::InternalBuffer#empty_to
0.21 0.02 79346 IO#external_encoding
0.21 0.03 79346 Kernel#String
0.21 0.02 80612 IO::InternalBuffer#full?
0.21 0.02 79346 BasicObject#!
0.10 0.00 80612 IO::InternalBuffer#unshift
-------------------------------------------------------
4.34 123.77 79346 BioPieces::Commands::write_fastq<123> {} [18]
[38] 0.1 1.12 6.05 79346 BioPieces::Seq#qual_convert! [38]
2.21 3.84 396730 Comparable#== [45]
-------------------------------------------------------
2.37 27.76 79346 BioPieces::Seq.new_bp [23]
[39] 0.1 1.30 5.78 317384 Hash#[] [39]
3.25 2.46 317384 Hash#find_item
0.08 0.00 79346 Hash#default
-------------------------------------------------------
1.59 8.20 79346 BioPieces::Seq#initialize [33]
[40] 0.1 1.06 5.86 317384 Hash#[] [40]
3.22 2.64 317384 Hash#find_item
-------------------------------------------------------
6.32 17.92 158692 IO#read [25]
[41] 0.1 0.80 5.59 158692 IO::InternalBuffer#fill_from [41]
1.33 4.26 158692 Rubinius.synchronize
-------------------------------------------------------
5.80 7.25 396730 Hash#[]= [29]
[42] 0.1 4.14 2.23 396730 Hash#new_bucket [42]
0.95 0.00 396730 Hash::Bucket#initialize
0.21 0.64 396730 Class#allocate
0.31 0.00 396730 Kernel#kind_of?
0.12 0.00 396730 Fixnum#+
-------------------------------------------------------
8.87 40.07 634768 String#+ [21]
[43] 0.1 4.97 1.27 634768 String.allocate [43]
0.55 0.00 634768 String#num_bytes=
0.37 0.00 634768 String.__allocate__
0.31 0.00 634768 Rubinius::ByteArray.allocate_sized
0.04 0.00 9 GC.collect_young
-------------------------------------------------------
9.56 26.55 79346 MessagePack.unpack [22]
[44] 0.1 1.74 4.44 317384 Hash#[] [44]
2.64 1.59 317384 Hash#find_item
0.21 0.00 238038 Hash#default
-------------------------------------------------------
1.12 6.05 79346 BioPieces::Seq#qual_convert! [38]
[45] 0.1 2.21 3.84 396730 Comparable#== [45]
1.46 1.77 158692 Symbol#<=>
0.39 0.05 158692 Comparable.compare_int
0.12 0.00 396730 Kernel#equal?
0.05 0.00 158692 Fixnum#==
-------------------------------------------------------
667 methods omitted
712 methods called a total of 0 times
===== Thread 8 =====
Total running time: 4858.171826775s
index % time self children called name
----------------------------------------------------------
[1] 100.0 0.00 4858.17 1 Thread#__run__ [1]
0.00 4858.17 1 Proc#call [2]
-------------------------------------------------------
0.00 4858.17 1 Thread#__run__ [1]
[2] 100.0 0.00 4858.17 1 Proc#call [2]
0.00 4858.17 1 BioPieces::Pipeline::run_thread<145> {} [3]
-------------------------------------------------------
0.00 4858.17 1 Proc#call [2]
[3] 100.0 0.00 4858.17 1 BioPieces::Pipeline::run_thread<145> {} [3]
0.00 4858.17 1 BioPieces::Pipeline::Command#run [4]
-------------------------------------------------------
0.00 4858.17 1 BioPieces::Pipeline::run_thread<145> {} [3]
[4] 100.0 0.00 4858.17 1 BioPieces::Pipeline::Command#run [4]
0.00 4858.05 1 Proc#call [5]
0.00 0.12 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4858.17 1 BioPieces::Pipeline::Command#run [4]
[5] 100.0 0.00 4858.05 1 Proc#call [5]
0.00 4858.05 1 BioPieces::Commands::plot_scores<116> {} [6]
-------------------------------------------------------
0.00 4858.05 1 Proc#call [5]
[6] 100.0 0.00 4858.05 1 BioPieces::Commands::plot_scores<116> {} [6]
0.00 4858.05 1 BioPieces::StatusHelper#status_track [7]
-------------------------------------------------------
0.00 4858.05 1 BioPieces::Commands::plot_scores<116> {} [6]
[7] 100.0 0.00 4858.05 1 BioPieces::StatusHelper#status_track [7]
0.00 4857.95 1 Proc#call [8]
0.00 0.10 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4858.05 1 BioPieces::StatusHelper#status_track [7]
[8] 100.0 0.00 4857.95 1 Proc#call [8]
0.00 4857.95 1 BioPieces::Commands::plot_scores<117> {} [9]
-------------------------------------------------------
0.00 4857.95 1 Proc#call [8]
[9] 100.0 0.00 4857.95 1 BioPieces::Commands::plot_scores<117> {} [9]
1.09 4856.49 1 BioPieces::Stream#each [10]
0.00 0.36 1 Gnuplot.open
-------------------------------------------------------
0.00 4857.95 1 BioPieces::Commands::plot_scores<117> {} [9]
[10] 100.0 1.09 4856.49 1 BioPieces::Stream#each [10]
0.80 4704.52 79347 IO#eof? [11]
7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
2.32 65.98 79346 BioPieces::Stream#read [17]
0.24 0.02 79347 BasicObject#!
-------------------------------------------------------
1.09 4856.49 1 BioPieces::Stream#each [10]
[11] 96.9 0.80 4704.52 79347 IO#eof? [11]
0.44 4703.45 79347 IO::InternalBuffer#fill_from [12]
0.51 0.08 79347 IO#ensure_open_and_readable
0.04 0.00 79348 IO::InternalBuffer#exhausted?
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
0.80 4704.52 79347 IO#eof? [11]
[12] 96.8 0.44 4703.45 79347 IO::InternalBuffer#fill_from [12]
0.86 4702.58 79347 Rubinius.synchronize [13]
-------------------------------------------------------
0.44 4703.45 79347 IO::InternalBuffer#fill_from [12]
[13] 96.8 0.86 4702.58 79347 Rubinius.synchronize [13]
2.18 4700.28 79347 IO::InternalBuffer::fill_from<73> {} [14]
0.07 0.00 79347 Rubinius.unlock
0.06 0.00 79347 Rubinius.lock
-------------------------------------------------------
0.86 4702.58 79347 Rubinius.synchronize [13]
[14] 96.8 2.18 4700.28 79347 IO::InternalBuffer::fill_from<73> {} [14]
4699.58 0.00 79347 IO::InternalBuffer#fill [15]
0.23 0.02 79347 IO::InternalBuffer#size
0.20 0.02 79347 IO::InternalBuffer#empty?
0.12 0.00 79347 IO::InternalBuffer#reset!
0.05 0.00 79347 IO::InternalBuffer#empty_to
0.03 0.00 79347 Fixnum#==
0.03 0.00 79347 Fixnum#<
-------------------------------------------------------
2.18 4700.28 79347 IO::InternalBuffer::fill_from<73> {} [14]
[15] 96.7 4699.58 0.00 79347 IO::InternalBuffer#fill [15]
-------------------------------------------------------
1.09 4856.49 1 BioPieces::Stream#each [10]
[16] 1.7 7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
1.42 21.80 79346 BioPieces::Stream#<< [20]
11.36 1.38 158692 NArray#[] [22]
10.12 1.47 158692 NArray#[]= [24]
1.22 6.27 317384 Hash#[] [26]
3.30 3.71 158692 NArray#+ [27]
2.09 4.03 79346 NArray#- [31]
2.19 0.97 158692 Hash#[]= [44]
1.50 0.07 79346 NArray.to_na
0.89 0.10 158692 Range#initialize
0.66 0.00 396737 String#length
-------------------------------------------------------
1.09 4856.49 1 BioPieces::Stream#each [10]
[17] 1.4 2.32 65.98 79346 BioPieces::Stream#read [17]
10.05 26.28 79346 MessagePack.unpack [18]
6.36 16.97 158692 IO#read [19]
1.31 1.45 79346 Hash#[]=
0.30 2.44 79346 Hash.new_from_literal
0.41 0.05 79346 Array#first
0.36 0.00 79346 String#unpack
-------------------------------------------------------
2.32 65.98 79346 BioPieces::Stream#read [17]
[18] 0.7 10.05 26.28 79346 MessagePack.unpack [18]
5.85 6.98 396730 Hash#[]= [21]
1.83 4.47 317384 Hash#[] [28]
0.56 3.15 79346 Class#new [38]
0.72 2.70 317384 Kernel#respond_to? [43]
0.03 0.00 79346 Kernel#kind_of?
-------------------------------------------------------
2.32 65.98 79346 BioPieces::Stream#read [17]
[19] 0.5 6.36 16.97 158692 IO#read [19]
0.75 5.43 158692 IO::InternalBuffer#fill_from [30]
0.72 3.68 158692 IO::InternalBuffer#shift [34]
1.25 1.07 158692 String#force_encoding
1.10 0.59 158692 String#<<
1.02 0.15 158692 IO#ensure_open_and_readable
0.39 0.05 158692 String#empty?
0.38 0.05 158692 BasicObject#!
0.15 0.00 317384 IO::InternalBuffer#exhausted?
0.14 0.00 476076 Fixnum#>
0.05 0.00 158692 Fixnum#-
-------------------------------------------------------
7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
[20] 0.5 1.42 21.80 79346 BioPieces::Stream#<< [20]
7.55 4.71 79346 MessagePack.pack [23]
3.04 5.98 158692 IO#write [25]
0.46 0.00 79346 Array#pack
0.05 0.00 79346 String#size
-------------------------------------------------------
10.05 26.28 79346 MessagePack.unpack [18]
[21] 0.3 5.85 6.98 396730 Hash#[]= [21]
4.08 2.00 396730 Hash#new_bucket [32]
0.21 0.02 79346 Hash::State#match?
0.16 0.00 396730 Rubinius::Tuple#[]
0.14 0.00 396730 Kernel#hash
0.13 0.00 396730 Fixnum#>
0.13 0.00 396730 Fixnum#&
0.12 0.00 317384 Rubinius::Tuple#[]=
-------------------------------------------------------
7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
[22] 0.3 11.36 1.38 158692 NArray#[] [22]
1.38 0.00 2697764 Kernel#kind_of?
-------------------------------------------------------
1.42 21.80 79346 BioPieces::Stream#<< [20]
[23] 0.3 7.55 4.71 79346 MessagePack.pack [23]
0.74 2.89 317384 Kernel#respond_to? [40]
0.49 0.13 79346 Hash#to_iter
0.41 0.00 476076 Hash::Iterator#next
0.03 0.00 79346 Kernel#kind_of?
0.02 0.00 3 GC.collect_young
-------------------------------------------------------
7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
[24] 0.2 10.12 1.47 158692 NArray#[]= [24]
1.47 0.00 2856456 Kernel#kind_of?
-------------------------------------------------------
1.42 21.80 79346 BioPieces::Stream#<< [20]
[25] 0.2 3.04 5.98 158692 IO#write [25]
1.06 0.81 158692 IO#binmode?
1.63 0.00 158692 IO#prim_write
0.95 0.16 158692 IO#ensure_open_and_writable
0.41 0.05 158692 Kernel#String
0.40 0.05 158692 IO#external_encoding
0.36 0.05 158692 BasicObject#!
0.05 0.00 158692 Fixnum#==
0.01 0.00 1 GC.collect_young
-------------------------------------------------------
7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
[26] 0.2 1.22 6.27 317384 Hash#[] [26]
3.64 2.63 317384 Hash#find_item [29]
-------------------------------------------------------
7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
[27] 0.1 3.30 3.71 158692 NArray#+ [27]
0.44 3.17 79346 Module#<= [41]
0.11 0.00 158692 Kernel#kind_of?
-------------------------------------------------------
10.05 26.28 79346 MessagePack.unpack [18]
[28] 0.1 1.83 4.47 317384 Hash#[] [28]
2.74 1.52 317384 Hash#find_item [35]
0.20 0.00 238038 Hash#default
-------------------------------------------------------
1.22 6.27 317384 Hash#[] [26]
[29] 0.1 3.64 2.63 317384 Hash#find_item [29]
1.29 0.18 317384 Hash::State#match?
0.83 0.09 317384 Hash#key_index
0.12 0.00 317384 Rubinius::Tuple#[]
0.11 0.00 317384 Kernel#hash
-------------------------------------------------------
6.36 16.97 158692 IO#read [19]
[30] 0.1 0.75 5.43 158692 IO::InternalBuffer#fill_from [30]
1.26 4.18 158692 Rubinius.synchronize [33]
-------------------------------------------------------
7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
[31] 0.1 2.09 4.03 79346 NArray#- [31]
0.48 3.46 79346 Module#<= [37]
0.10 0.00 79346 Kernel#kind_of?
-------------------------------------------------------
5.85 6.98 396730 Hash#[]= [21]
[32] 0.1 4.08 2.00 396730 Hash#new_bucket [32]
0.93 0.00 396730 Hash::Bucket#initialize
0.18 0.46 396730 Class#allocate
0.29 0.00 396730 Kernel#kind_of?
0.12 0.00 396730 Fixnum#+
-------------------------------------------------------
0.75 5.43 158692 IO::InternalBuffer#fill_from [30]
[33] 0.1 1.26 4.18 158692 Rubinius.synchronize [33]
2.34 1.65 158692 IO::InternalBuffer::fill_from<73> {} [36]
0.10 0.00 158692 Rubinius.lock
0.08 0.00 158692 Rubinius.unlock
-------------------------------------------------------
6.36 16.97 158692 IO#read [19]
[34] 0.1 0.72 3.68 158692 IO::InternalBuffer#shift [34]
1.08 2.59 158692 Rubinius.synchronize [39]
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
1.83 4.47 317384 Hash#[] [28]
[35] 0.1 2.74 1.52 317384 Hash#find_item [35]
0.79 0.09 317384 Hash#key_index
0.35 0.05 79346 Hash::State#match?
0.13 0.00 317384 Rubinius::Tuple#[]
0.11 0.00 317384 Kernel#hash
-------------------------------------------------------
1.26 4.18 158692 Rubinius.synchronize [33]
[36] 0.1 2.34 1.65 158692 IO::InternalBuffer::fill_from<73> {} [36]
0.58 0.00 78974 IO::InternalBuffer#fill
0.41 0.05 158692 IO::InternalBuffer#empty?
0.33 0.04 158692 IO::InternalBuffer#size
0.10 0.00 78974 IO::InternalBuffer#reset!
0.09 0.00 158692 IO::InternalBuffer#empty_to
0.02 0.00 78974 Fixnum#==
0.02 0.00 78974 Fixnum#<
-------------------------------------------------------
2.09 4.03 79346 NArray#- [31]
[37] 0.1 0.48 3.46 79346 Module#<= [37]
0.70 2.73 79346 Module#< [42]
0.03 0.00 79346 Kernel#equal?
-------------------------------------------------------
10.05 26.28 79346 MessagePack.unpack [18]
[38] 0.1 0.56 3.15 79346 Class#new [38]
0.44 1.20 79346 Hash.allocate
0.83 0.68 79346 Hash#initialize
-------------------------------------------------------
0.72 3.68 158692 IO::InternalBuffer#shift [34]
[39] 0.1 1.08 2.59 158692 Rubinius.synchronize [39]
1.76 0.67 158692 IO::InternalBuffer::shift<162> {}
0.08 0.00 158692 Rubinius.lock
0.08 0.00 158692 Rubinius.unlock
-------------------------------------------------------
7.55 4.71 79346 MessagePack.pack [23]
[40] 0.1 0.74 2.89 317384 Kernel#respond_to? [40]
2.73 0.15 317384 Kernel#respond_to_prim?
-------------------------------------------------------
3.30 3.71 158692 NArray#+ [27]
[41] 0.1 0.44 3.17 79346 Module#<= [41]
0.67 2.48 79346 Module#< [45]
0.02 0.00 79346 Kernel#equal?
-------------------------------------------------------
0.48 3.46 79346 Module#<= [37]
[42] 0.1 0.70 2.73 79346 Module#< [42]
1.82 0.83 79346 Rubinius::Type.each_ancestor
0.05 0.00 79346 Kernel#kind_of?
0.03 0.00 79346 Kernel#equal?
-------------------------------------------------------
10.05 26.28 79346 MessagePack.unpack [18]
[43] 0.1 0.72 2.70 317384 Kernel#respond_to? [43]
2.54 0.16 317384 Kernel#respond_to_prim?
-------------------------------------------------------
7.67 74.94 79346 BioPieces::Commands::plot_scores<118> {} [16]
[44] 0.1 2.19 0.97 158692 Hash#[]= [44]
0.66 0.09 158692 Hash::State#match?
0.06 0.00 158692 Rubinius::Tuple#[]
0.05 0.00 158692 Kernel#hash
0.05 0.00 158692 Fixnum#&
0.05 0.00 158692 Fixnum#>
-------------------------------------------------------
0.44 3.17 79346 Module#<= [41]
[45] 0.1 0.67 2.48 79346 Module#< [45]
1.66 0.75 79346 Rubinius::Type.each_ancestor
0.05 0.00 79346 Kernel#kind_of?
0.03 0.00 79346 Kernel#equal?
-------------------------------------------------------
583 methods omitted
628 methods called a total of 0 times
===== Thread 9 =====
Total running time: 4857.58611215s
index % time self children called name
----------------------------------------------------------
[1] 100.0 0.00 4857.59 1 Thread#__run__ [1]
0.00 4857.59 1 Proc#call [2]
-------------------------------------------------------
0.00 4857.59 1 Thread#__run__ [1]
[2] 100.0 0.00 4857.59 1 Proc#call [2]
0.00 4857.59 1 BioPieces::Pipeline::run_thread<145> {} [3]
-------------------------------------------------------
0.00 4857.59 1 Proc#call [2]
[3] 100.0 0.00 4857.59 1 BioPieces::Pipeline::run_thread<145> {} [3]
0.00 4857.59 1 BioPieces::Pipeline::Command#run [4]
-------------------------------------------------------
0.00 4857.59 1 BioPieces::Pipeline::run_thread<145> {} [3]
[4] 100.0 0.00 4857.59 1 BioPieces::Pipeline::Command#run [4]
0.00 4857.57 1 Proc#call [5]
0.00 0.02 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4857.59 1 BioPieces::Pipeline::Command#run [4]
[5] 100.0 0.00 4857.57 1 Proc#call [5]
0.00 4857.57 1 BioPieces::Commands::grab<150> {} [6]
-------------------------------------------------------
0.00 4857.57 1 Proc#call [5]
[6] 100.0 0.00 4857.57 1 BioPieces::Commands::grab<150> {} [6]
0.00 4857.57 1 BioPieces::StatusHelper#status_track [7]
-------------------------------------------------------
0.00 4857.57 1 BioPieces::Commands::grab<150> {} [6]
[7] 100.0 0.00 4857.57 1 BioPieces::StatusHelper#status_track [7]
0.00 4857.55 1 Proc#call [8]
0.00 0.01 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4857.57 1 BioPieces::StatusHelper#status_track [7]
[8] 100.0 0.00 4857.55 1 Proc#call [8]
0.00 4857.55 1 BioPieces::Commands::grab<151> {} [9]
-------------------------------------------------------
0.00 4857.55 1 Proc#call [8]
[9] 100.0 0.00 4857.55 1 BioPieces::Commands::grab<151> {} [9]
5.07 4852.48 1 BioPieces::Stream#each [10]
-------------------------------------------------------
0.00 4857.55 1 BioPieces::Commands::grab<151> {} [9]
[10] 100.0 5.07 4852.48 1 BioPieces::Stream#each [10]
3.53 4428.93 370639 IO#eof? [11]
10.54 312.28 370638 BioPieces::Stream#read [16]
8.85 86.95 370638 BioPieces::Commands::grab<157> {} [19]
1.25 0.12 370639 BasicObject#!
0.02 0.00 2 GC.collect_young
-------------------------------------------------------
5.07 4852.48 1 BioPieces::Stream#each [10]
[11] 91.2 3.53 4428.93 370639 IO#eof? [11]
1.92 4424.07 370639 IO::InternalBuffer#fill_from [12]
2.40 0.35 370639 IO#ensure_open_and_readable
0.19 0.00 370640 IO::InternalBuffer#exhausted?
-------------------------------------------------------
3.53 4428.93 370639 IO#eof? [11]
[12] 91.1 1.92 4424.07 370639 IO::InternalBuffer#fill_from [12]
3.73 4420.34 370639 Rubinius.synchronize [13]
-------------------------------------------------------
1.92 4424.07 370639 IO::InternalBuffer#fill_from [12]
[13] 91.1 3.73 4420.34 370639 Rubinius.synchronize [13]
9.75 4410.08 370639 IO::InternalBuffer::fill_from<73> {} [14]
0.30 0.00 370639 Rubinius.unlock
0.21 0.00 370639 Rubinius.lock
-------------------------------------------------------
3.73 4420.34 370639 Rubinius.synchronize [13]
[14] 91.0 9.75 4410.08 370639 IO::InternalBuffer::fill_from<73> {} [14]
4406.88 0.00 370637 IO::InternalBuffer#fill [15]
1.11 0.11 370639 IO::InternalBuffer#size
0.87 0.11 370639 IO::InternalBuffer#empty?
0.53 0.00 370637 IO::InternalBuffer#reset!
0.23 0.00 370639 IO::InternalBuffer#empty_to
0.13 0.00 370637 Fixnum#==
0.12 0.00 370637 Fixnum#<
-------------------------------------------------------
9.75 4410.08 370639 IO::InternalBuffer::fill_from<73> {} [14]
[15] 90.7 4406.88 0.00 370637 IO::InternalBuffer#fill [15]
-------------------------------------------------------
5.07 4852.48 1 BioPieces::Stream#each [10]
[16] 6.6 10.54 312.28 370638 BioPieces::Stream#read [16]
47.49 125.61 370638 MessagePack.unpack [17]
28.47 79.39 741276 IO#read [18]
1.29 12.59 370638 Hash.new_from_literal [38]
6.22 7.01 370638 Hash#[]= [40]
2.06 0.27 370638 Array#first
1.85 0.00 370638 String#unpack
0.03 0.00 5 GC.collect_young
-------------------------------------------------------
10.54 312.28 370638 BioPieces::Stream#read [16]
[17] 3.6 47.49 125.61 370638 MessagePack.unpack [17]
27.92 33.14 1853055 Hash#[]= [20]
8.63 20.63 1482552 Hash#[] [23]
3.55 14.12 1482552 Kernel#respond_to? [33]
2.72 14.76 370638 Class#new [34]
0.14 0.00 370638 Kernel#kind_of?
0.01 0.00 2 GC.collect_young
0.00 0.00 1 GC.collect_mature
-------------------------------------------------------
10.54 312.28 370638 BioPieces::Stream#read [16]
[18] 2.2 28.47 79.39 741276 IO#read [18]
3.57 24.95 741276 IO::InternalBuffer#fill_from [26]
3.29 17.19 741276 IO::InternalBuffer#shift [29]
5.91 4.98 741276 String#force_encoding
5.17 2.97 741276 String#<<
4.85 0.73 741276 IO#ensure_open_and_readable
1.86 0.22 741276 BasicObject#!
1.80 0.22 741276 String#empty?
0.66 0.00 2223828 Fixnum#>
0.66 0.00 1482552 IO::InternalBuffer#exhausted?
0.21 0.00 741276 Fixnum#-
-------------------------------------------------------
5.07 4852.48 1 BioPieces::Stream#each [10]
[19] 2.0 8.85 86.95 370638 BioPieces::Commands::grab<157> {} [19]
1.76 33.23 370638 BioPieces::Commands#grab_regexes [21]
1.49 22.31 79346 BioPieces::Stream#<< [28]
4.34 13.82 820622 Hash#[] [32]
5.93 2.65 449984 Hash#[]=
1.13 0.13 370638 BasicObject#!
0.14 0.00 449984 Fixnum#+
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
47.49 125.61 370638 MessagePack.unpack [17]
[20] 1.3 27.92 33.14 1853055 Hash#[]= [20]
19.43 9.56 1853055 Hash#new_bucket [24]
0.96 0.11 370503 Hash::State#match?
0.74 0.00 1853055 Rubinius::Tuple#[]
0.61 0.00 1853055 Kernel#hash
0.60 0.00 1853055 Fixnum#>
0.56 0.00 1482552 Rubinius::Tuple#[]=
0.55 0.00 1853055 Fixnum#&
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
8.85 86.95 370638 BioPieces::Commands::grab<157> {} [19]
[21] 0.7 1.76 33.23 370638 BioPieces::Commands#grab_regexes [21]
4.14 29.08 370638 Array#each [22]
-------------------------------------------------------
1.76 33.23 370638 BioPieces::Commands#grab_regexes [21]
[22] 0.7 4.14 29.08 370638 Array#each [22]
2.84 25.73 370638 BioPieces::Commands::grab_regexes<267> {} [25]
0.19 0.00 661930 Fixnum#+
0.19 0.00 661930 Fixnum#<
0.13 0.00 370638 Rubinius::Tuple#at
-------------------------------------------------------
47.49 125.61 370638 MessagePack.unpack [17]
[23] 0.6 8.63 20.63 1482552 Hash#[] [23]
12.50 7.14 1482552 Hash#find_item [30]
0.98 0.00 1111914 Hash#default
-------------------------------------------------------
27.92 33.14 1853055 Hash#[]= [20]
[24] 0.6 19.43 9.56 1853055 Hash#new_bucket [24]
4.39 0.00 1853055 Hash::Bucket#initialize
0.90 2.33 1853055 Class#allocate
1.38 0.00 1853055 Kernel#kind_of?
0.55 0.00 1853055 Fixnum#+
0.01 0.00 1 GC.collect_young
-------------------------------------------------------
4.14 29.08 370638 Array#each [22]
[25] 0.6 2.84 25.73 370638 BioPieces::Commands::grab_regexes<267> {} [25]
4.06 12.97 370638 Array#each [36]
1.39 7.31 370638 Hash#[]
-------------------------------------------------------
28.47 79.39 741276 IO#read [18]
[26] 0.6 3.57 24.95 741276 IO::InternalBuffer#fill_from [26]
5.86 19.09 741276 Rubinius.synchronize [27]
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
3.57 24.95 741276 IO::InternalBuffer#fill_from [26]
[27] 0.5 5.86 19.09 741276 Rubinius.synchronize [27]
10.64 7.56 741276 IO::InternalBuffer::fill_from<73> {} [31]
0.49 0.00 741276 Rubinius.lock
0.41 0.00 741276 Rubinius.unlock
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
8.85 86.95 370638 BioPieces::Commands::grab<157> {} [19]
[28] 0.5 1.49 22.31 79346 BioPieces::Stream#<< [28]
7.80 4.55 79346 MessagePack.pack [43]
3.13 6.20 158692 IO#write
0.57 0.00 79346 Array#pack
0.05 0.00 79346 String#size
-------------------------------------------------------
28.47 79.39 741276 IO#read [18]
[29] 0.4 3.29 17.19 741276 IO::InternalBuffer#shift [29]
4.93 12.23 741276 Rubinius.synchronize [35]
0.03 0.00 3 GC.collect_young
-------------------------------------------------------
8.63 20.63 1482552 Hash#[] [23]
[30] 0.4 12.50 7.14 1482552 Hash#find_item [30]
3.65 0.45 1482552 Hash#key_index
1.69 0.22 370638 Hash::State#match?
0.61 0.00 1482552 Rubinius::Tuple#[]
0.52 0.00 1482552 Kernel#hash
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
5.86 19.09 741276 Rubinius.synchronize [27]
[31] 0.4 10.64 7.56 741276 IO::InternalBuffer::fill_from<73> {} [31]
2.63 0.00 370280 IO::InternalBuffer#fill
1.78 0.22 741276 IO::InternalBuffer#empty?
1.57 0.21 741276 IO::InternalBuffer#size
0.48 0.00 370280 IO::InternalBuffer#reset!
0.44 0.00 741276 IO::InternalBuffer#empty_to
0.11 0.00 370280 Fixnum#==
0.11 0.00 370280 Fixnum#<
0.01 0.00 3 GC.collect_young
-------------------------------------------------------
8.85 86.95 370638 BioPieces::Commands::grab<157> {} [19]
[32] 0.4 4.34 13.82 820622 Hash#[] [32]
8.27 5.18 820622 Hash#find_item [39]
0.36 0.00 370638 Hash#default
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
47.49 125.61 370638 MessagePack.unpack [17]
[33] 0.4 3.55 14.12 1482552 Kernel#respond_to? [33]
13.35 0.77 1482552 Kernel#respond_to_prim? [37]
-------------------------------------------------------
47.49 125.61 370638 MessagePack.unpack [17]
[34] 0.4 2.72 14.76 370638 Class#new [34]
3.99 3.42 370638 Hash#initialize
2.07 5.29 370638 Hash.allocate
-------------------------------------------------------
3.29 17.19 741276 IO::InternalBuffer#shift [29]
[35] 0.4 4.93 12.23 741276 Rubinius.synchronize [35]
8.22 3.23 741276 IO::InternalBuffer::shift<162> {} [44]
0.40 0.00 741276 Rubinius.lock
0.38 0.00 741276 Rubinius.unlock
-------------------------------------------------------
2.84 25.73 370638 BioPieces::Commands::grab_regexes<267> {} [25]
[36] 0.4 4.06 12.97 370638 Array#each [36]
1.29 11.15 370638 BioPieces::Commands::grab_regexes<269> {} [42]
0.19 0.00 661930 Fixnum#<
0.19 0.00 661930 Fixnum#+
0.15 0.00 370638 Rubinius::Tuple#at
-------------------------------------------------------
3.55 14.12 1482552 Kernel#respond_to? [33]
[37] 0.3 13.35 0.77 1482552 Kernel#respond_to_prim? [37]
0.77 0.00 1482552 Kernel#respond_to_missing?
-------------------------------------------------------
10.54 312.28 370638 BioPieces::Stream#read [16]
[38] 0.3 1.29 12.59 370638 Hash.new_from_literal [38]
2.24 10.35 370638 Hash.allocate [41]
-------------------------------------------------------
4.34 13.82 820622 Hash#[] [32]
[39] 0.3 8.27 5.18 820622 Hash#find_item [39]
2.08 0.24 820622 Hash#key_index
1.99 0.27 449984 Hash::State#match?
0.30 0.00 820622 Rubinius::Tuple#[]
0.29 0.00 820622 Kernel#hash
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
10.54 312.28 370638 BioPieces::Stream#read [16]
[40] 0.3 6.22 7.01 370638 Hash#[]= [40]
4.41 1.91 370638 Hash#new_bucket
0.17 0.00 370638 Kernel#hash
0.16 0.00 370638 Rubinius::Tuple#[]=
0.15 0.00 370638 Rubinius::Tuple#[]
0.11 0.00 370638 Fixnum#>
0.11 0.00 370638 Fixnum#&
-------------------------------------------------------
1.29 12.59 370638 Hash.new_from_literal [38]
[41] 0.3 2.24 10.35 370638 Hash.allocate [41]
4.51 1.23 370638 Hash#__setup__
0.35 4.25 370638 Class#allocate
-------------------------------------------------------
4.06 12.97 370638 Array#each [36]
[42] 0.3 1.29 11.15 370638 BioPieces::Commands::grab_regexes<269> {} [42]
3.32 7.83 370638 String#=~ [45]
-------------------------------------------------------
1.49 22.31 79346 BioPieces::Stream#<< [28]
[43] 0.3 7.80 4.55 79346 MessagePack.pack [43]
0.74 2.75 317384 Kernel#respond_to?
0.49 0.12 79346 Hash#to_iter
0.44 0.00 476076 Hash::Iterator#next
0.03 0.00 79346 Kernel#kind_of?
-------------------------------------------------------
4.93 12.23 741276 Rubinius.synchronize [35]
[44] 0.2 8.22 3.23 741276 IO::InternalBuffer::shift<162> {} [44]
1.55 0.21 741276 IO::InternalBuffer#size
1.01 0.00 741276 String.from_bytearray
0.23 0.00 741276 Fixnum#+
0.21 0.00 741276 Fixnum#<
0.02 0.00 4 GC.collect_young
-------------------------------------------------------
1.29 11.15 370638 BioPieces::Commands::grab_regexes<269> {} [42]
[45] 0.2 3.32 7.83 370638 String#=~ [45]
4.26 0.00 370638 Regexp#search_region
0.84 1.27 79346 MatchData#begin
1.06 0.17 370638 Module#===
0.24 0.00 370638 Regexp.last_match=
-------------------------------------------------------
256 methods omitted
301 methods called a total of 0 times
===== Thread 10 =====
Total running time: 4857.550991351s
index % time self children called name
----------------------------------------------------------
[1] 100.0 0.00 4857.55 1 Thread#__run__ [1]
0.00 4857.55 1 Proc#call [2]
-------------------------------------------------------
0.00 4857.55 1 Thread#__run__ [1]
[2] 100.0 0.00 4857.55 1 Proc#call [2]
0.00 4857.55 1 BioPieces::Pipeline::run_thread<145> {} [3]
-------------------------------------------------------
0.00 4857.55 1 Proc#call [2]
[3] 100.0 0.00 4857.55 1 BioPieces::Pipeline::run_thread<145> {} [3]
0.00 4857.55 1 BioPieces::Pipeline::Command#run [4]
-------------------------------------------------------
0.00 4857.55 1 BioPieces::Pipeline::run_thread<145> {} [3]
[4] 100.0 0.00 4857.55 1 BioPieces::Pipeline::Command#run [4]
0.00 4857.53 1 Proc#call [5]
0.00 0.02 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4857.55 1 BioPieces::Pipeline::Command#run [4]
[5] 100.0 0.00 4857.53 1 Proc#call [5]
0.00 4857.53 1 BioPieces::Commands::mean_scores<98> {} [6]
-------------------------------------------------------
0.00 4857.53 1 Proc#call [5]
[6] 100.0 0.00 4857.53 1 BioPieces::Commands::mean_scores<98> {} [6]
0.00 4857.53 1 BioPieces::StatusHelper#status_track [7]
-------------------------------------------------------
0.00 4857.53 1 BioPieces::Commands::mean_scores<98> {} [6]
[7] 100.0 0.00 4857.53 1 BioPieces::StatusHelper#status_track [7]
0.00 4857.52 1 Proc#call [8]
0.00 0.01 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4857.53 1 BioPieces::StatusHelper#status_track [7]
[8] 100.0 0.00 4857.52 1 Proc#call [8]
0.00 4857.52 1 BioPieces::Commands::mean_scores<99> {} [9]
-------------------------------------------------------
0.00 4857.52 1 Proc#call [8]
[9] 100.0 0.00 4857.52 1 BioPieces::Commands::mean_scores<99> {} [9]
5.16 4852.36 1 BioPieces::Stream#each [10]
-------------------------------------------------------
0.00 4857.52 1 BioPieces::Commands::mean_scores<99> {} [9]
[10] 100.0 5.16 4852.36 1 BioPieces::Stream#each [10]
3.66 4097.00 370639 IO#eof? [11]
19.04 426.61 370638 BioPieces::Commands::mean_scores<100> {} [16]
10.52 294.21 370638 BioPieces::Stream#read [17]
1.20 0.12 370639 BasicObject#!
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
5.16 4852.36 1 BioPieces::Stream#each [10]
[11] 84.4 3.66 4097.00 370639 IO#eof? [11]
2.04 4092.26 370639 IO::InternalBuffer#fill_from [12]
2.18 0.34 370639 IO#ensure_open_and_readable
0.19 0.00 370640 IO::InternalBuffer#exhausted?
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
3.66 4097.00 370639 IO#eof? [11]
[12] 84.3 2.04 4092.26 370639 IO::InternalBuffer#fill_from [12]
3.71 4088.54 370639 Rubinius.synchronize [13]
-------------------------------------------------------
2.04 4092.26 370639 IO::InternalBuffer#fill_from [12]
[13] 84.2 3.71 4088.54 370639 Rubinius.synchronize [13]
9.49 4078.51 370639 IO::InternalBuffer::fill_from<73> {} [14]
0.31 0.00 370639 Rubinius.unlock
0.24 0.00 370639 Rubinius.lock
-------------------------------------------------------
3.71 4088.54 370639 Rubinius.synchronize [13]
[14] 84.2 9.49 4078.51 370639 IO::InternalBuffer::fill_from<73> {} [14]
4075.39 0.00 370638 IO::InternalBuffer#fill [15]
1.02 0.11 370639 IO::InternalBuffer#size
0.86 0.11 370639 IO::InternalBuffer#empty?
0.56 0.00 370638 IO::InternalBuffer#reset!
0.23 0.00 370639 IO::InternalBuffer#empty_to
0.12 0.00 370638 Fixnum#==
0.12 0.00 370638 Fixnum#<
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
9.49 4078.51 370639 IO::InternalBuffer::fill_from<73> {} [14]
[15] 83.9 4075.39 0.00 370638 IO::InternalBuffer#fill [15]
-------------------------------------------------------
5.16 4852.36 1 BioPieces::Stream#each [10]
[16] 9.2 19.04 426.61 370638 BioPieces::Commands::mean_scores<100> {} [16]
11.74 129.76 370503 BioPieces::Seq.new_bp [19]
6.61 95.59 370638 BioPieces::Stream#<< [21]
5.96 59.21 370503 BioPieces::Seq#scores_mean [22]
15.26 27.27 370503 Float#round [27]
8.21 32.99 1853055 Hash#[] [29]
16.87 14.17 1111779 Hash#[]= [33]
2.59 0.00 370638 String#length
0.22 0.00 741276 Fixnum#+
0.11 0.00 370638 Fixnum#>
0.04 0.00 7 GC.collect_young
-------------------------------------------------------
5.16 4852.36 1 BioPieces::Stream#each [10]
[17] 6.3 10.52 294.21 370638 BioPieces::Stream#read [17]
44.72 110.07 370638 MessagePack.unpack [18]
30.30 79.39 741276 IO#read [20]
5.94 6.97 370638 Hash#[]=
1.40 11.50 370638 Hash.new_from_literal
1.92 0.26 370638 Array#first
1.73 0.00 370638 String#unpack
0.01 0.00 2 GC.collect_young
-------------------------------------------------------
10.52 294.21 370638 BioPieces::Stream#read [17]
[18] 3.2 44.72 110.07 370638 MessagePack.unpack [18]
20.91 25.61 1482552 Hash#[]= [24]
8.58 20.06 1482552 Hash#[] [34]
3.30 14.25 1482552 Kernel#respond_to?
2.72 14.50 370638 Class#new
0.14 0.00 370638 Kernel#kind_of?
-------------------------------------------------------
19.04 426.61 370638 BioPieces::Commands::mean_scores<100> {} [16]
[19] 2.9 11.74 129.76 370503 BioPieces::Seq.new_bp [19]
19.78 25.65 1482012 Hash#[]= [25]
7.81 35.73 370503 BioPieces::Seq#initialize [26]
6.30 26.26 1482012 Hash#[] [31]
1.19 6.86 370503 Hash.new_from_literal
0.17 0.00 370503 Class#allocate
-------------------------------------------------------
10.52 294.21 370638 BioPieces::Stream#read [17]
[20] 2.3 30.30 79.39 741276 IO#read [20]
3.52 24.98 741276 IO::InternalBuffer#fill_from [35]
3.35 17.21 741276 IO::InternalBuffer#shift [44]
5.93 5.13 741276 String#force_encoding
5.32 2.89 741276 String#<<
4.50 0.72 741276 IO#ensure_open_and_readable
1.93 0.22 741276 BasicObject#!
1.85 0.22 741276 String#empty?
0.67 0.00 1482552 IO::InternalBuffer#exhausted?
0.66 0.00 2223828 Fixnum#>
0.21 0.00 741276 Fixnum#-
-------------------------------------------------------
19.04 426.61 370638 BioPieces::Commands::mean_scores<100> {} [16]
[21] 2.1 6.61 95.59 370638 BioPieces::Stream#<< [21]
31.66 19.48 370638 MessagePack.pack [23]
13.74 28.14 741276 IO#write [28]
2.33 0.00 370638 Array#pack
0.24 0.00 370638 String#size
-------------------------------------------------------
19.04 426.61 370638 BioPieces::Commands::mean_scores<100> {} [16]
[22] 1.3 5.96 59.21 370503 BioPieces::Seq#scores_mean [22]
9.11 17.67 370503 NArray#- [37]
6.90 17.30 370503 NArray#mean [41]
7.73 0.32 370503 NArray.to_na
0.19 0.00 370503 Kernel#nil?
-------------------------------------------------------
6.61 95.59 370638 BioPieces::Stream#<< [21]
[23] 1.1 31.66 19.48 370638 MessagePack.pack [23]
3.32 11.32 1482552 Kernel#respond_to?
2.21 0.49 370638 Hash#to_iter
1.97 0.00 2223693 Hash::Iterator#next
0.14 0.00 370638 Kernel#kind_of?
0.03 0.00 4 GC.collect_young
0.00 0.00 1 GC.collect_mature
-------------------------------------------------------
44.72 110.07 370638 MessagePack.unpack [18]
[24] 1.0 20.91 25.61 1482552 Hash#[]= [24]
15.51 7.63 1482552 Hash#new_bucket [43]
0.58 0.00 1482552 Rubinius::Tuple#[]
0.54 0.00 1482552 Rubinius::Tuple#[]=
0.49 0.00 1482552 Kernel#hash
0.44 0.00 1482552 Fixnum#>
0.44 0.00 1482552 Fixnum#&
-------------------------------------------------------
11.74 129.76 370503 BioPieces::Seq.new_bp [19]
[25] 0.9 19.78 25.65 1482012 Hash#[]= [25]
15.25 7.94 1482012 Hash#new_bucket [42]
0.57 0.00 1482012 Rubinius::Tuple#[]
0.54 0.00 1482012 Rubinius::Tuple#[]=
0.48 0.00 1482012 Kernel#hash
0.43 0.00 1482012 Fixnum#&
0.43 0.00 1482012 Fixnum#>
0.01 0.00 1 GC.collect_young
-------------------------------------------------------
11.74 129.76 370503 BioPieces::Seq.new_bp [19]
[26] 0.9 7.81 35.73 370503 BioPieces::Seq#initialize [26]
5.03 27.05 1482012 Hash#[] [32]
2.52 0.00 741006 String#length
1.02 0.11 370503 BasicObject#!=
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
19.04 426.61 370638 BioPieces::Commands::mean_scores<100> {} [16]
[27] 0.9 15.26 27.27 370503 Float#round [27]
2.49 22.19 370503 Math.frexp [40]
0.51 0.00 1111509 Fixnum#divide
0.27 0.00 370503 Float#*
0.22 0.00 741006 Fixnum#+
0.22 0.00 741006 Fixnum#<
0.22 0.00 370503 Float#infinite?
0.21 0.00 741006 Fixnum#>
0.19 0.00 370503 Fixnum#to_f
0.15 0.00 370503 Float#nan?
0.14 0.00 370503 Fixnum#**
-------------------------------------------------------
6.61 95.59 370638 BioPieces::Stream#<< [21]
[28] 0.9 13.74 28.14 741276 IO#write [28]
4.78 3.79 741276 IO#binmode?
8.46 0.00 741276 IO#prim_write
4.00 0.68 741276 IO#ensure_open_and_writable
1.95 0.26 741276 Kernel#String
1.81 0.21 741276 IO#external_encoding
1.75 0.22 741276 BasicObject#!
0.22 0.00 741276 Fixnum#==
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
19.04 426.61 370638 BioPieces::Commands::mean_scores<100> {} [16]
[29] 0.8 8.21 32.99 1853055 Hash#[] [29]
19.13 13.52 1853055 Hash#find_item [30]
0.35 0.00 370503 Hash#default
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
8.21 32.99 1853055 Hash#[] [29]
[30] 0.7 19.13 13.52 1853055 Hash#find_item [30]
6.12 0.86 1482552 Hash::State#match?
4.61 0.56 1853055 Hash#key_index
0.74 0.00 1853055 Rubinius::Tuple#[]
0.63 0.00 1853055 Kernel#hash
-------------------------------------------------------
11.74 129.76 370503 BioPieces::Seq.new_bp [19]
[31] 0.7 6.30 26.26 1482012 Hash#[] [31]
15.27 10.63 1482012 Hash#find_item [38]
0.35 0.00 370503 Hash#default
0.01 0.00 1 GC.collect_young
-------------------------------------------------------
7.81 35.73 370503 BioPieces::Seq#initialize [26]
[32] 0.7 5.03 27.05 1482012 Hash#[] [32]
15.36 11.69 1482012 Hash#find_item [36]
-------------------------------------------------------
19.04 426.61 370638 BioPieces::Commands::mean_scores<100> {} [16]
[33] 0.6 16.87 14.17 1111779 Hash#[]= [33]
4.22 3.95 370503 Hash#new_bucket
3.95 0.54 1111779 Hash::State#match?
0.42 0.00 1111779 Rubinius::Tuple#[]
0.37 0.00 1111779 Kernel#hash
0.33 0.00 1111779 Fixnum#>
0.33 0.00 1111779 Fixnum#&
0.06 0.00 8 GC.collect_young
-------------------------------------------------------
44.72 110.07 370638 MessagePack.unpack [18]
[34] 0.6 8.58 20.06 1482552 Hash#[] [34]
12.10 6.97 1482552 Hash#find_item [45]
0.98 0.00 1111914 Hash#default
-------------------------------------------------------
30.30 79.39 741276 IO#read [20]
[35] 0.6 3.52 24.98 741276 IO::InternalBuffer#fill_from [35]
5.68 19.30 741276 Rubinius.synchronize [39]
-------------------------------------------------------
5.03 27.05 1482012 Hash#[] [32]
[36] 0.6 15.36 11.69 1482012 Hash#find_item [36]
5.72 0.86 1482012 Hash::State#match?
3.62 0.43 1482012 Hash#key_index
0.57 0.00 1482012 Rubinius::Tuple#[]
0.49 0.00 1482012 Kernel#hash
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
5.96 59.21 370503 BioPieces::Seq#scores_mean [22]
[37] 0.6 9.11 17.67 370503 NArray#- [37]
2.04 15.16 370503 Module#<=
0.46 0.00 370503 Kernel#kind_of?
-------------------------------------------------------
6.30 26.26 1482012 Hash#[] [31]
[38] 0.5 15.27 10.63 1482012 Hash#find_item [38]
4.94 0.74 1482012 Hash::State#match?
3.44 0.43 1482012 Hash#key_index
0.59 0.00 1482012 Rubinius::Tuple#[]
0.49 0.00 1482012 Kernel#hash
-------------------------------------------------------
3.52 24.98 741276 IO::InternalBuffer#fill_from [35]
[39] 0.5 5.68 19.30 741276 Rubinius.synchronize [39]
10.85 7.61 741276 IO::InternalBuffer::fill_from<73> {}
0.46 0.00 741276 Rubinius.lock
0.38 0.00 741276 Rubinius.unlock
-------------------------------------------------------
15.26 27.27 370503 Float#round [27]
[40] 0.5 2.49 22.19 370503 Math.frexp [40]
8.10 8.89 370503 Rubinius::FFI::MemoryPointer.new
2.39 2.78 370503 Rubinius::Type.coerce_to_float
0.02 0.00 4 GC.collect_young
-------------------------------------------------------
5.96 59.21 370503 BioPieces::Seq#scores_mean [22]
[41] 0.5 6.90 17.30 370503 NArray#mean [41]
5.10 0.00 370503 NArray#sum
3.96 0.00 370503 NArray#to_type
2.98 0.61 370503 NArray#rank_total
2.21 0.45 370503 NArray#integer?
1.69 0.00 370503 NArray.ref
0.31 0.00 370503 Float#/
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
19.78 25.65 1482012 Hash#[]= [25]
[42] 0.5 15.25 7.94 1482012 Hash#new_bucket [42]
3.58 0.00 1482012 Hash::Bucket#initialize
0.77 2.09 1482012 Class#allocate
1.04 0.00 1482012 Kernel#kind_of?
0.44 0.00 1482012 Fixnum#+
0.01 0.00 1 GC.collect_young
-------------------------------------------------------
20.91 25.61 1482552 Hash#[]= [24]
[43] 0.5 15.51 7.63 1482552 Hash#new_bucket [43]
3.69 0.00 1482552 Hash::Bucket#initialize
0.74 1.62 1482552 Class#allocate
1.14 0.00 1482552 Kernel#kind_of?
0.44 0.00 1482552 Fixnum#+
-------------------------------------------------------
30.30 79.39 741276 IO#read [20]
[44] 0.4 3.35 17.21 741276 IO::InternalBuffer#shift [44]
4.97 12.24 741276 Rubinius.synchronize
0.01 0.00 3 GC.collect_young
-------------------------------------------------------
8.58 20.06 1482552 Hash#[] [34]
[45] 0.4 12.10 6.97 1482552 Hash#find_item [45]
3.59 0.43 1482552 Hash#key_index
1.64 0.22 370638 Hash::State#match?
0.59 0.00 1482552 Rubinius::Tuple#[]
0.50 0.00 1482552 Kernel#hash
-------------------------------------------------------
350 methods omitted
395 methods called a total of 0 times
===== Thread 11 =====
Total running time: 4857.522190238s
index % time self children called name
----------------------------------------------------------
[1] 100.0 0.00 4857.52 1 Thread#__run__ [1]
0.00 4857.52 1 Proc#call [2]
-------------------------------------------------------
0.00 4857.52 1 Thread#__run__ [1]
[2] 100.0 0.00 4857.52 1 Proc#call [2]
0.00 4857.52 1 BioPieces::Pipeline::run_thread<145> {} [3]
-------------------------------------------------------
0.00 4857.52 1 Proc#call [2]
[3] 100.0 0.00 4857.52 1 BioPieces::Pipeline::run_thread<145> {} [3]
0.00 4857.52 1 BioPieces::Pipeline::Command#run [4]
-------------------------------------------------------
0.00 4857.52 1 BioPieces::Pipeline::run_thread<145> {} [3]
[4] 100.0 0.00 4857.52 1 BioPieces::Pipeline::Command#run [4]
0.00 4857.50 1 Proc#call [5]
0.00 0.02 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4857.52 1 BioPieces::Pipeline::Command#run [4]
[5] 100.0 0.00 4857.50 1 Proc#call [5]
0.00 4857.50 1 BioPieces::Commands::trim_seq<110> {} [6]
-------------------------------------------------------
0.00 4857.50 1 Proc#call [5]
[6] 100.0 0.00 4857.50 1 BioPieces::Commands::trim_seq<110> {} [6]
0.00 4857.50 1 BioPieces::StatusHelper#status_track [7]
-------------------------------------------------------
0.00 4857.50 1 BioPieces::Commands::trim_seq<110> {} [6]
[7] 100.0 0.00 4857.50 1 BioPieces::StatusHelper#status_track [7]
0.00 4857.48 1 Proc#call [8]
0.00 0.02 1 BioPieces::StatusHelper#status_save
-------------------------------------------------------
0.00 4857.50 1 BioPieces::StatusHelper#status_track [7]
[8] 100.0 0.00 4857.48 1 Proc#call [8]
0.00 4857.48 1 BioPieces::Commands::trim_seq<111> {} [9]
-------------------------------------------------------
0.00 4857.48 1 Proc#call [8]
[9] 100.0 0.00 4857.48 1 BioPieces::Commands::trim_seq<111> {} [9]
4.97 4852.52 1 BioPieces::Stream#each [10]
-------------------------------------------------------
0.00 4857.48 1 BioPieces::Commands::trim_seq<111> {} [9]
[10] 100.0 4.97 4852.52 1 BioPieces::Stream#each [10]
3.62 3909.44 370639 IO#eof? [11]
34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
10.18 277.89 370638 BioPieces::Stream#read [17]
1.16 0.13 370639 BasicObject#!
-------------------------------------------------------
4.97 4852.52 1 BioPieces::Stream#each [10]
[11] 80.6 3.62 3909.44 370639 IO#eof? [11]
1.93 3904.69 370639 IO::InternalBuffer#fill_from [12]
2.28 0.33 370639 IO#ensure_open_and_readable
0.20 0.00 370640 IO::InternalBuffer#exhausted?
-------------------------------------------------------
3.62 3909.44 370639 IO#eof? [11]
[12] 80.4 1.93 3904.69 370639 IO::InternalBuffer#fill_from [12]
3.42 3901.26 370639 Rubinius.synchronize [13]
0.01 0.00 3 GC.collect_young
-------------------------------------------------------
1.93 3904.69 370639 IO::InternalBuffer#fill_from [12]
[13] 80.4 3.42 3901.26 370639 Rubinius.synchronize [13]
8.51 3892.26 370639 IO::InternalBuffer::fill_from<73> {} [14]
0.27 0.00 370639 Rubinius.unlock
0.22 0.00 370639 Rubinius.lock
-------------------------------------------------------
3.42 3901.26 370639 Rubinius.synchronize [13]
[14] 80.3 8.51 3892.26 370639 IO::InternalBuffer::fill_from<73> {} [14]
3889.24 0.00 368216 IO::InternalBuffer#fill [15]
0.94 0.11 370639 IO::InternalBuffer#size
0.87 0.11 370639 IO::InternalBuffer#empty?
0.54 0.00 368216 IO::InternalBuffer#reset!
0.23 0.00 370639 IO::InternalBuffer#empty_to
0.12 0.00 368216 Fixnum#==
0.11 0.00 368216 Fixnum#<
-------------------------------------------------------
8.51 3892.26 370639 IO::InternalBuffer::fill_from<73> {} [14]
[15] 80.1 3889.24 0.00 368216 IO::InternalBuffer#fill [15]
-------------------------------------------------------
4.97 4852.52 1 BioPieces::Stream#each [10]
[16] 13.4 34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
11.48 130.57 370638 BioPieces::Seq.new_bp [19]
1.53 133.49 370638 BioPieces::Trim#quality_trim! [20]
6.40 94.36 370638 BioPieces::Stream#<< [23]
13.35 74.03 3706380 Hash#[] [25]
7.04 52.30 370638 BioPieces::Seq#to_bp [27]
31.86 14.87 2223828 Hash#[]= [31]
1.95 36.86 370638 Hash#merge! [37]
4.10 0.78 741276 BioPieces::Seq#length
0.70 0.00 2223828 Fixnum#+
0.12 0.00 370638 Kernel#===
-------------------------------------------------------
4.97 4852.52 1 BioPieces::Stream#each [10]
[17] 5.9 10.18 277.89 370638 BioPieces::Stream#read [17]
40.97 107.78 370638 MessagePack.unpack [18]
29.22 72.73 741276 IO#read [22]
5.67 6.45 370638 Hash#[]=
1.27 10.12 370638 Hash.new_from_literal
1.83 0.26 370638 Array#first
1.56 0.00 370638 String#unpack
0.03 0.00 7 GC.collect_young
-------------------------------------------------------
10.18 277.89 370638 BioPieces::Stream#read [17]
[18] 3.1 40.97 107.78 370638 MessagePack.unpack [18]
20.26 25.35 1482552 Hash#[]= [32]
8.35 20.13 1482552 Hash#[] [42]
2.55 14.51 370638 Class#new
3.33 13.16 1482552 Kernel#respond_to?
0.13 0.00 370638 Kernel#kind_of?
-------------------------------------------------------
34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
[19] 2.9 11.48 130.57 370638 BioPieces::Seq.new_bp [19]
8.19 38.73 370638 BioPieces::Seq#initialize [30]
19.21 23.81 1482552 Hash#[]= [33]
6.11 26.30 1482552 Hash#[] [40]
1.20 6.85 370638 Hash.new_from_literal
0.17 0.00 370638 Class#allocate
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
[20] 2.8 1.53 133.49 370638 BioPieces::Trim#quality_trim! [20]
9.90 123.59 370638 BioPieces::Trim#quality_trim [21]
-------------------------------------------------------
1.53 133.49 370638 BioPieces::Trim#quality_trim! [20]
[21] 2.7 9.90 123.59 370638 BioPieces::Trim#quality_trim [21]
6.95 89.01 370638 BioPieces::Seq#[] [24]
6.07 11.73 370638 BioPieces::Trim#check_trim_args
4.04 0.61 741276 BioPieces::Seq#length
2.20 0.00 370638 BioPieces::Trim#trim_right_pos_c
1.78 0.23 370638 Range#initialize
0.57 0.00 370638 BioPieces::Trim#trim_left_pos_c
0.19 0.00 370638 Class#allocate
0.11 0.00 370638 Fixnum#>
0.11 0.00 22 GC.collect_young
-------------------------------------------------------
10.18 277.89 370638 BioPieces::Stream#read [17]
[22] 2.1 29.22 72.73 741276 IO#read [22]
3.55 20.53 741276 IO::InternalBuffer#fill_from
3.23 16.77 741276 IO::InternalBuffer#shift
5.72 4.93 741276 String#force_encoding
4.77 2.65 741276 String#<<
4.34 0.70 741276 IO#ensure_open_and_readable
1.77 0.22 741276 String#empty?
1.76 0.21 741276 BasicObject#!
0.66 0.00 1482552 IO::InternalBuffer#exhausted?
0.65 0.00 2223828 Fixnum#>
0.21 0.00 741276 Fixnum#-
-------------------------------------------------------
34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
[23] 2.1 6.40 94.36 370638 BioPieces::Stream#<< [23]
31.22 20.07 370638 MessagePack.pack [28]
13.57 27.08 741276 IO#write [35]
2.18 0.00 370638 Array#pack
0.22 0.00 370638 String#size
0.01 0.00 1 GC.collect_young
-------------------------------------------------------
9.90 123.59 370638 BioPieces::Trim#quality_trim [21]
[24] 2.0 6.95 89.01 370638 BioPieces::Seq#[] [24]
30.59 18.73 741276 String#[] [29]
5.92 33.40 370638 BioPieces::Seq#initialize [36]
0.18 0.00 370638 Kernel#nil?
0.16 0.00 370638 Class#allocate
0.01 0.00 4 GC.collect_young
-------------------------------------------------------
34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
[25] 1.8 13.35 74.03 3706380 Hash#[] [25]
42.40 31.63 3706380 Hash#find_item [26]
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
13.35 74.03 3706380 Hash#[] [25]
[26] 1.5 42.40 31.63 3706380 Hash#find_item [26]
16.46 2.35 4447656 Hash::State#match?
8.90 1.07 3706380 Hash#key_index
1.56 0.00 3706380 Rubinius::Tuple#[]
1.27 0.00 3706380 Kernel#hash
0.01 0.00 5 GC.collect_young
-------------------------------------------------------
34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
[27] 1.2 7.04 52.30 370638 BioPieces::Seq#to_bp [27]
19.37 23.17 1482552 Hash#[]= [34]
1.23 8.40 370638 Hash.new_from_literal
0.13 0.00 370638 String#length
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
6.40 94.36 370638 BioPieces::Stream#<< [23]
[28] 1.1 31.22 20.07 370638 MessagePack.pack [28]
3.42 12.01 1482552 Kernel#respond_to?
2.30 0.50 370638 Hash#to_iter
1.67 0.00 1853190 Hash::Iterator#next
0.12 0.00 370638 Kernel#kind_of?
0.06 0.00 10 GC.collect_young
0.00 0.00 2 GC.collect_mature
-------------------------------------------------------
6.95 89.01 370638 BioPieces::Seq#[] [24]
[29] 1.0 30.59 18.73 741276 String#[] [29]
5.16 1.32 2223828 Module#===
3.26 0.49 1482552 Rubinius::Type.coerce_to
1.94 0.21 741276 Range#first
1.81 0.21 741276 Range#last
1.63 0.00 741276 String#substring
0.85 0.00 2965104 Fixnum#<
0.67 0.00 2223828 String#size
0.42 0.00 1482552 Fixnum#>
0.22 0.00 741276 Kernel#equal?
0.21 0.00 741276 Fixnum#==
-------------------------------------------------------
11.48 130.57 370638 BioPieces::Seq.new_bp [19]
[30] 1.0 8.19 38.73 370638 BioPieces::Seq#initialize [30]
5.16 27.29 1482552 Hash#[] [39]
5.13 0.00 741276 String#length
1.04 0.11 370638 BasicObject#!=
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
[31] 1.0 31.86 14.87 2223828 Hash#[]= [31]
10.46 1.49 2965104 Hash::State#match?
0.90 0.00 2223828 Rubinius::Tuple#[]
0.72 0.00 2223828 Kernel#hash
0.66 0.00 2223828 Fixnum#&
0.64 0.00 2223828 Fixnum#>
0.01 0.00 3 GC.collect_young
0.00 0.00 1 GC.collect_mature
-------------------------------------------------------
40.97 107.78 370638 MessagePack.unpack [18]
[32] 0.9 20.26 25.35 1482552 Hash#[]= [32]
15.20 7.71 1482552 Hash#new_bucket
0.56 0.00 1482552 Rubinius::Tuple#[]
0.54 0.00 1482552 Rubinius::Tuple#[]=
0.48 0.00 1482552 Kernel#hash
0.43 0.00 1482552 Fixnum#>
0.43 0.00 1482552 Fixnum#&
-------------------------------------------------------
11.48 130.57 370638 BioPieces::Seq.new_bp [19]
[33] 0.9 19.21 23.81 1482552 Hash#[]= [33]
14.74 6.61 1482552 Hash#new_bucket
0.58 0.00 1482552 Rubinius::Tuple#[]
0.54 0.00 1482552 Rubinius::Tuple#[]=
0.48 0.00 1482552 Kernel#hash
0.43 0.00 1482552 Fixnum#&
0.42 0.00 1482552 Fixnum#>
-------------------------------------------------------
7.04 52.30 370638 BioPieces::Seq#to_bp [27]
[34] 0.9 19.37 23.17 1482552 Hash#[]= [34]
14.81 5.89 1482552 Hash#new_bucket
0.57 0.00 1482552 Rubinius::Tuple#[]
0.56 0.00 1482552 Rubinius::Tuple#[]=
0.48 0.00 1482552 Kernel#hash
0.43 0.00 1482552 Fixnum#&
0.43 0.00 1482552 Fixnum#>
0.00 0.00 2 GC.collect_young
-------------------------------------------------------
6.40 94.36 370638 BioPieces::Stream#<< [23]
[35] 0.8 13.57 27.08 741276 IO#write [35]
4.68 3.83 741276 IO#binmode?
7.60 0.00 741276 IO#prim_write
4.15 0.68 741276 IO#ensure_open_and_writable
1.82 0.21 741276 IO#external_encoding
1.71 0.25 741276 Kernel#String
1.71 0.21 741276 BasicObject#!
0.22 0.00 741276 Fixnum#==
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
6.95 89.01 370638 BioPieces::Seq#[] [24]
[36] 0.8 5.92 33.40 370638 BioPieces::Seq#initialize [36]
8.66 16.20 1482552 Hash#[]
1.31 7.16 370638 Hash.new_from_literal
0.08 0.00 13 GC.collect_young
-------------------------------------------------------
34.31 615.80 370638 BioPieces::Commands::trim_seq<119> {} [16]
[37] 0.8 1.95 36.86 370638 Hash#merge! [37]
4.98 31.87 370638 Hash#each_item [38]
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
1.95 36.86 370638 Hash#merge! [37]
[38] 0.8 4.98 31.87 370638 Hash#each_item [38]
5.55 26.24 1482552 Hash::merge!<423> {} [41]
0.08 0.00 18 GC.collect_young
-------------------------------------------------------
8.19 38.73 370638 BioPieces::Seq#initialize [30]
[39] 0.7 5.16 27.29 1482552 Hash#[] [39]
15.68 11.61 1482552 Hash#find_item [43]
-------------------------------------------------------
11.48 130.57 370638 BioPieces::Seq.new_bp [19]
[40] 0.7 6.11 26.30 1482552 Hash#[] [40]
15.41 10.55 1482552 Hash#find_item [45]
0.35 0.00 370638 Hash#default
-------------------------------------------------------
4.98 31.87 370638 Hash#each_item [38]
[41] 0.7 5.55 26.24 1482552 Hash::merge!<423> {} [41]
17.65 8.56 1482552 Hash#[]= [44]
0.03 0.00 5 GC.collect_young
-------------------------------------------------------
40.97 107.78 370638 MessagePack.unpack [18]
[42] 0.6 8.35 20.13 1482552 Hash#[] [42]
12.29 6.86 1482552 Hash#find_item
0.98 0.00 1111914 Hash#default
-------------------------------------------------------
5.16 27.29 1482552 Hash#[] [39]
[43] 0.6 15.68 11.61 1482552 Hash#find_item [43]
5.68 0.86 1482552 Hash::State#match?
3.56 0.43 1482552 Hash#key_index
0.59 0.00 1482552 Rubinius::Tuple#[]
0.48 0.00 1482552 Kernel#hash
0.00 0.00 1 GC.collect_mature
0.00 0.00 1 GC.collect_young
-------------------------------------------------------
5.55 26.24 1482552 Hash::merge!<423> {} [41]
[44] 0.5 17.65 8.56 1482552 Hash#[]= [44]
5.76 0.85 1482552 Hash::State#match?
0.57 0.00 1482552 Rubinius::Tuple#[]
0.47 0.00 1482552 Kernel#hash
0.43 0.00 1482552 Fixnum#&
0.43 0.00 1482552 Fixnum#>
0.04 0.00 9 GC.collect_young
-------------------------------------------------------
6.11 26.30 1482552 Hash#[] [40]
[45] 0.5 15.41 10.55 1482552 Hash#find_item [45]
4.96 0.75 1482552 Hash::State#match?
3.32 0.43 1482552 Hash#key_index
0.60 0.00 1482552 Rubinius::Tuple#[]
0.49 0.00 1482552 Kernel#hash
-------------------------------------------------------
402 methods omitted
447 methods called a total of 0 times
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