Question: Question: SAM-to-BAM: fatal exit code Error 139
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gravatar for annadv77
2.7 years ago by
annadv7720
Canada
annadv7720 wrote:

Dear All,

I am analyzing DNAseq data. I obtained a SAM file by using "Map with BWA for Illumina data". However, when I try to transform that SAM file into BAM file, using "SAM-to-BAM" module, it stops and says:

Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No such file or directory: '/galaxy-repl/main/jobdir/010/521/10521429/__dataset_21432079_metadata_temp_file_S37hQZ.bai' Fatal error: Exit code 139 (Error) /galaxy-repl/main/

Could anyone, please, suggest what is the problem and how to solve this?

I'm running the public instance of Galaxy (http://usegalaxy.org).

 

Thank you very much!

 

Regards,

Anna

 

sam dnaseq bam • 905 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by annadv7720
0
gravatar for annadv77
2.7 years ago by
annadv7720
Canada
annadv7720 wrote:

Dear All,

I think that I've found the source of the problem I was having - although I did obtain the SAM file, the alignment was very poor, with very low MAPQ scores (0s), so if I understand correctly, that would mean, that the alignments were not unique, and that is probably why I could not obtain a BAM file.

I think that the reason for the poor alignment was the fact, that the sequence contained repetitive short sequences, which interfered with the alignment.

 

Regards,

Anna

ADD COMMENTlink written 2.7 years ago by annadv7720
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