Hi Alan, Thanks for the gdb trace, I will look into this. -Kanwei On Tue, Dec 14, 2010 at 11:30 PM, Alan Jackson <alan@netvalue.net.nz> wrote:

Hi,

I've been trying to use the Trackster visualisation with a BAM file, and find it segfaults quite regularly, with the (somewhat unhelpful) message

./run.sh: line 47: 13782 Segmentation fault      (core dumped) python ./scripts/paster.py serve universe_wsgi.ini $@

Using gdb I have gotten the following info:

Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x4a6b5940 (LWP 13800)] 0x00002adeee8c7937 in get_chunk_coordinates (idx=0xffffffffb0018da0, tid=0, beg=0, end=-1341883296,   cnt_off=0x2aaab0016600) at samtools/bam_index.c:501 501     samtools/bam_index.c: No such file or directory.       in samtools/bam_index.c

However the BAM index should be getting created and stored as part of the meta data.

I also notice the pysam library being used is 0.1.1, whereas they are up to 0.3.1.

Any help greatly appreciated, the visualisation looks very good when it's working.

I am able to send the BAM file I'm using if necessary.

Cheers, --Alan _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev