Hi, Could you possibly share your history with me (making sure to include all of the files you used to get to the point where it fails) at kpvincent@bx.psu.edu ? I can't really tell what the problem is from this error. There appear to be a couple of things wrong (the index of the BAM file doesn't get created and then Samtools seg faults when it tries to index the reference file). With your actual files, I can look into the failures in more depth. Regards, Kelly On Nov 8, 2009, at 9:50 PM, galaxy-bugs@bx.psu.edu wrote:

GALAXY TOOL ERROR REPORT ------------------------

This error report was sent from the Galaxy instance hosted on the server "main.g2.bx.psu.edu" ----------------------------------------------------------------------------- This is in reference to output dataset 913904. ----------------------------------------------------------------------------- The user 'u4705270@hotmail.com' provided the following information: I have problem when I use SAM file from BWA to transform to BAM in SAM tool. sh: line 1: 32286 Segmentation fault samtools faidx /galaxy/ home/g2main/galaxy_main/database/tmp/framework/tmpGSqkyx 2> /dev/null sh: line 1: 32291 Segmentation fault samtools sort /galaxy/home/ g2main/galaxy_main/database/tmp/framework/tmpdokBYv /galaxy/home/ g2main/galaxy_main/database/tmp/framework/tmpU-Dbdm 2> /dev/null lseek: Invalid argument [bam_header_read] read from pipe; skip EOF checking. There was a problem creating the index for the BAM file

----------------------------------------------------------------------------- job id: 676933 tool id: sam_to_bam ----------------------------------------------------------------------------- job stderr: sh: line 1: 32286 Segmentation fault samtools faidx /galaxy/ home/g2main/galaxy_main/database/tmp/framework/tmpGSqkyx 2> /dev/null sh: line 1: 32291 Segmentation fault samtools sort /galaxy/home/ g2main/galaxy_main/database/tmp/framework/tmpdokBYv /galaxy/home/ g2main/galaxy_main/database/tmp/framework/tmpU-Dbdm 2> /dev/null lseek: Invalid argument [bam_header_read] read from pipe; skip EOF checking. There was a problem creating the index for the BAM file

----------------------------------------------------------------------------- job stdout:

----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message). _______________________________________________ galaxy-bugs mailing list galaxy-bugs@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-bugs