Open olgabot opened 9 years ago
Here's the error from GATK Queue:
INFO 09:27:32,735 QCommandLine - Done with errors INFO 09:27:32,760 QGraph - ------- INFO 09:27:32,760 QGraph - Failed: 'samtools' 'index' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD023_GAGTGG_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD023_GAGTGG_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai' INFO 09:27:32,761 QGraph - Log: /home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD023_GAGTGG_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai.out INFO 09:27:32,761 QGraph - ------- INFO 09:27:32,761 QGraph - Failed: 'samtools' 'index' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD010_TAGCTT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD010_TAGCTT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai' INFO 09:27:32,762 QGraph - Log: /home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD010_TAGCTT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai.out INFO 09:27:32,762 QGraph - ------- INFO 09:27:32,762 QGraph - Failed: 'samtools' 'index' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD027_ATTCCT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD027_ATTCCT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai' INFO 09:27:32,763 QGraph - Log: /home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD027_ATTCCT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai.out INFO 09:27:32,763 QGraph - ------- INFO 09:27:32,763 QGraph - Failed: 'samtools' 'index' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD025_ACTGAT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD025_ACTGAT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai' INFO 09:27:32,764 QGraph - Log: /home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD025_ACTGAT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai.out INFO 09:27:32,775 QCommandLine - Script failed with 91 total jobs [obotvinnik@tscc-1-37 scripts]$ ess /home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD025_ACTGAT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai.out l-bash: ess: command not found
Here's the log file:
[obotvinnik@tscc-1-37 scripts]$ less /home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD025_ACTGAT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai.out Samtools-htslib-API: bam_index_build2() not yet implemented /home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/.queue/tmp/.exec3472088511571501657: line 2: 5074 Aborted 'samtools' 'index' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD025_ACTGAT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam' '/home/obotvinnik/projects/20150609_ys_rbfox2kd/analysis/20150609_ys_rbfox2kd_v1/AD025_ACTGAT_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai' Nodes: tscc-2-48
Here's the error from GATK Queue:
Here's the log file: