Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Question: SAM-to-BAM: fatal exit code Error 139
0
gravatar for annadv77
3.1 years ago by
annadv77 • 20
Canada
annadv77 • 20 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 • 1.1k views
ADD COMMENT • link •
modified 3.1 years ago • written 3.1 years ago by annadv77 • 20
0
gravatar for annadv77
3.1 years ago by
annadv77 • 20
Canada
annadv77 • 20 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 COMMENT • link written 3.1 years ago by annadv77 • 20
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour