Question: Problem co-ordinate sorting BAM file with Galaxy
0
gravatar for nash.claire
2.2 years ago by
nash.claire230
Canada
nash.claire230 wrote:

Hi everyone,

Sorry to bother all you experts again but I have another "newbie" problem. Please help!!

I want to filter my BAM sequencing files to get rid of all alignments that map to regions such as chrM etc. I've tried using the "Filter SAM/BAM, output SAM/BAM" module for this and by inputting into the Select region parameter chr1, chr2 etc etc (to include all 22 plus X and Y). However I keep getting the error message:-

[bam_index_core] the alignment is not sorted (NS500375:111:HCM3KBGXX:1:21112:6686:13429): 134945990 > 72989 in 2-th chr [bam_index_build2] fail to index the BAM file. *** glibc detected *** python: double free or corruption (!prev): 0x00000000077c6440 **

I thought this would be due to the fact that my BAM files are not co-ordinate sorted. I've tried running the SortSam module (Picard tools) and this didn't fix the problem. I then tied the Sort module (SAM tools) and this didn't fix it either. 

I'm stuck. Can anyone help? Galaxy only solutions please, I can't use R, Python etc yet unfortunately. 

Thanks in advance

ADD COMMENTlink modified 24 months ago by Biostar ♦♦ 20 • written 2.2 years ago by nash.claire230

One of our researchers also ran into this problem last week with SortSam itself, Galaxy Picard tools.  From the command line, as Galaxy (server app) user, running exactly the same command line call that the Galaxy tool ran, the SortSam command executes without generating an error.  So its something about the Galaxy environment configuration?  Hard for a non-pro to solve because it is a glibc c++ error inside a python script called by picard java...!  I don't have a solution.

ADD REPLYlink written 2.1 years ago by damion.dooley0

I just found this thread which may be related: https://biostar.usegalaxy.org/p/13021/#14405

And a Galaxy trouble ticket: https://trello.com/c/lwAdo5NG/2732-sorting-bam-by-queryname-query-is-problematic-with-both-sort-tools

 

Damion

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by damion.dooley0
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