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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: