Open pawanchk opened 9 months ago
Hi there, I am no longer on this project, but it looks like there may be an issue with the data.
STDERR: [ERROR] (src/bam_access.c: reads_at_pos_callback:843 errno: No such file or directory) Error, strand was already found for this readname HWI-ST118_106002510:3:23:14898:144717.
implies that this read may have both ends mapped to the same orientation, which wouldn't be 'properly paired' by definition. Are you able to check sam flags for this read pair? Have you altered the acceptable flags required for CaVEMan to include a read in analysis at all?
If you can share the contents of ~/result/tmpCaveman/caveman.cfg.ini
or your initial commandline for the setup step they may help.
Hi,
I am using
caveman.pl
with Whole Exome sequencing (WXS) data however the execution ends in an error in themstep
process (please see the error below), this error occurs for various regions and then the execution stops.I am using the singularity image created from the docker image to execute
caveman.pl
. For WGS data, the analysis completes successfully but for WXS data, it ends in this error.Can I please know how to overcome this error ?