accopeland

 # GAA
 120         bitbucket.org:berkeleylab/jgi-gaag.git
 121         # Portal
 122         https://bitbucket.org/berkeleylab/jgi-portal-libraries
 123         https://bitbucket.org/berkeleylab/jgi-genome-portal
 124         # SDM
 125         https://bitbucket.org/htandra/jgi-kbase-es
 126         https://bitbucket.org/berkeleylab/jgi-lapinpy
 127         https://bitbucket.org/berkeleylab/jgi-sdm-ncbi
 128         https://bitbucket.org/berkeleylab/jgi-sdm-pacbio

accopeland

diff --git a/src/signals-apple.c b/src/signals-apple.c
index ab3709b..5001166 100644
--- a/src/signals-apple.c
+++ b/src/signals-apple.c
@@ -9,7 +9,7 @@
 #include <sys/_types/_ucontext64.h>
 #else
 #define __need_ucontext64_t
-#include <machine/_structs.h>
+#include <sys/_structs.h>

accopeland

gcc (GCC) 4.8.1
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

GNU assembler (GNU Binutils) 2.25
Copyright (C) 2014 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or later.
This program has absolutely no warranty.

accopeland

> uname -a
Linux gpint110 2.6.32-431.46.2.el6.nersc.x86_64 #1 SMP Thu Jan 22 09:48:18 PST 2015 x86_64 GNU/Linux

> git --version
git version 1.7.2.5

> gcc --version
gcc (GCC) 4.6.3

accopeland

> time run_kraken APAHO.1000.fa --fasta-input
kraken --threads 16 --db /scratch/copeland/kraken_db/standard --output kraken.APAHO.1000.out --fasta-input APAHO.1000.fa
1000 sequences (0.15 Mbp) processed in 0.073s (819.6 Kseq/m, 123.77 Mbp/m).
  10 sequences classified (1.00%)
  990 sequences unclassified (99.00%)
kraken-report --db /scratch/copeland/kraken_db/standard kraken.APAHO.1000.out
kraken-translate --db /scratch/copeland/kraken_db/standard kraken.APAHO.1000.out
kraken-mpa-report --db /scratch/copeland/kraken_db/standard kraken.APAHO.1000.out

real    0m42.860s

accopeland

> time blastn -query tadpole.Mru_no0-9.MDA.bbnorm.k75.asm.fasta -db refseq.archaea/refseq.archaea -outfmt 6 -out blastn.tadpole.Mru_no0-9.MDA.bbnorm.k75.asm.fasta.v.refseq.archaea.out -evalue 1e-6 -num_alignments 10 -num_threads 1

real    0m8.932s
user    0m8.527s
sys     0m0.407s
copeland@gpint110:/scratch/copeland> time blastn -query tadpole.Mru_no0-9.MDA.bbnorm.k75.asm.fasta -db refseq.archaea/refseq.archaea -outfmt 6 -out blastn.tadpole.Mru_no0-9.MDA.bbnorm.k75.asm.fasta.v.refseq.archaea.out -evalue 1e-6 -num_alignments 10 -num_threads 4

real    0m3.380s
user    0m10.243s
sys     0m0.430s

accopeland

/scratch/copeland> time run_blastn APAHO.4M.fa mydb/human -word_size=38
# module load blast+ && blastn -query APAHO.4M.fa -db mydb/human -outfmt 6 -out blastn.APAHO.4M.fa.v.human.out -evalue 1e-6 -num_alignments 10 -num_threads 8 -word_size=38

real    28m14.418s
user    91m21.060s
sys     2m55.572s

accopeland

start, 2015-10-28 21:26:23
ktrim start, 2015-10-28 21:26:23
ktrim finish, 2015-10-28 21:27:37
filter start, 2015-10-28 21:27:37
filter finish, 2015-10-28 21:28:43
delete temp files start, 2015-10-28 21:28:43
delete temp files finish, 2015-10-28 21:28:44
dehumanize start, 2015-10-28 21:28:44
dehumanize finish, 2015-10-28 21:35:40
delete temp files start, 2015-10-28 21:35:40