Alright, I'm at a loss

I can run the sam to bam converter on a small sam file but not a big sam file. The small SAM file is only 65K, the big SAM file is 44G. I have more than 8TB of free space.


Running the job script from the shell results in the small conversion succeeding and the big one failing. The return code from samtools in both instances in 0 so I can't for any reason think of why there the script is getting caught in an exception.

I even added a write statement to stdout to double-check the return code and stderr message and they are the same in both cases.

Why is this failing in one case and not the other?  I'm stuck.  Help....

Ryan

On 4/6/11 4:58 PM, Ryan Golhar wrote:
So it looks like I can get small sam files converted to bam files, but
not large sam files (~50GB-80GB). I'm still trying to debug this, but
not sure what's going on.

Has anyone else run into anything like this?


On 4/6/11 10:08 AM, Ryan Golhar wrote:
Any ideas why I would get this? If I run the sam_to_bam python script
from the shell, I get the same error:

(galaxy_env)[galaxy@vail pbs]$ sh 471.sh
Linux vail 2.6.18-194.3.1.el5xen #1 SMP Sun May 2 04:26:43 EDT 2010 x8
6_64 x86_64 x86_64 GNU/Linux
Samtools Version: 0.1.14 (r933:170)
Error extracting alignments from
(/home/galaxy/galaxy-dist/database/files/000/dataset_785.dat),

However running the samtools command works fine

On 4/5/11 5:58 PM, Ryan Golhar wrote:
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?

Ryan
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