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YeoLab / gscripts

General Use Scripts and Helper functions
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Rna-Seq pipeline breaks while indexing bam file #66

Closed shassathe closed 9 years ago

shassathe commented 9 years ago

RNa-Seq pipeline fails during indexing of bam file. Here's the error:

samtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools) samtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools) Samtools-htslib-API: bam_index_build2() not yet implemented

olgabot commented 9 years ago

What's the command that causes the error?

On Tue, Mar 31, 2015 at 8:58 AM Shashank Sathe notifications@github.com wrote:

RNa-Seq pipeline fails during indexing of bam file. Here's the error:

samtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools) samtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools) Samtools-htslib-API: bam_index_build2() not yet implemented

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/66.

shassathe commented 9 years ago

samtools index Here's the log:

INFO 09:45:24,076 QGraph - Failed: 'samtools' 'index' '/oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I6/CV-B_MN_UT_no_NHS_2_AGTCAA_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam' '/oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I6/CV-B_MN_UT_no_NHS_2_AGTCAA_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai'

INFO 09:45:24,076 QGraph - Log: /oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I6/CV-B_MN_UT_no_NHS_2_AGTCAA_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai.out

The output file specifies the error: "Samtools-htslib-API: bam_index_build2() not yet implemented"

olgabot commented 9 years ago

Yep, I'm getting the same error.

$ 'samtools' 'index' '/oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I6/CV-B_MN_UT_no_NHS_2_AGTCAA_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam' '/oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I6/CV-B_MN_UT_no_NHS_2_AGTCAA_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai'
samtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools)
samtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools)
Samtools-htslib-API: bam_index_build2() not yet implemented
Aborted

This isn't using our own samtools, which might be the problem.

$ which samtools
/opt/biotools/samtools/bin/samtools