I've performed an alignment using BWA on a file of paired-end illumina reads. The SAM file looks fine, and contains header information. I'm converting it to BAM using the sam to bam converter, however it consistently errors out after running for a while. The error is:

"Error extracting alignments from (/home/galaxy/galaxy-dist/database/files/000/dataset_785.dat), "

but no error is provided. Looking at the sam_to_bam.py on line 156 is where the error is thrown. Nothing is in e (I think).

BTW - If I run the samtools command from the shell by hand, the BAM file is created properly. I do see information on stderr:

$ samtools view -bt /data/genomes/H_sapiens/hg19/hg19.fa.fai -o /tmp/killme.bam /home/galaxy/galaxy-dist/database/files/000/dataset_785.dat
[samopen] SAM header is present: 25 sequences.

I'm using samtools version 0.1.14 (r933:170) on Linux, 64-bit.

What do I do?

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