analyze_rna_seq.scala breaks at `samtools index`

[olgabot]

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