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comparison test-data/samblaster.txt @ 0:b437798cb165 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
author iuc
date Tue, 24 Oct 2017 06:29:40 -0400
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-1:000000000000 0:b437798cb165
1 samblaster: Version 0.1.22
2 samblaster: Inputting from stdin
3 samblaster: Outputting to stdout
4 samblaster: Opening /vagrant/test-out6/virtual-normal-samblaster-markdups.txt for write.
5 [bam_header_read] EOF marker is absent. The input is probably truncated.
6 [M::mem_pestat] skip orientation FF as there are not enough pairs
7 [M::mem_pestat] skip orientation FR as there are not enough pairs
8 [M::mem_pestat] skip orientation RF as there are not enough pairs
9 [M::mem_pestat] skip orientation RR as there are not enough pairs
10 samblaster: Loaded 86 header sequence entries.
11 samblaster: Removed 1 of 78 (1.28%) read ids as duplicates using 1724k memory in 0.000S CPU seconds and 31S wall time.
12 [main] Version: 0.7.7-r441
13 [main] CMD:[samopen] SAM header is present: 86 sequences.
14 bwa mem -M -v 1 -R @RG\tID:virtual-normal\tSM:virtual-normal\tLB:virtual-normal\tPL:ILLUMINA -t 2 /proj/b2010040/private/nobackup/autoseq-genome/bwa/human_g1k_v37_decoy.fasta /vagrant/test-out6/skewer/virtual-normal_1.fastq.gz /vagrant/test-out6/skewer/virtual-normal_2.fastq.gz
15 [main] Real time: 30.780 sec; CPU: 13.292 sec