This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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> |
This file has been truncated, but you can view the full file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
> 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
> 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
> 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
/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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 |