Question: Problem with the Filter SAM/BAM module
gravatar for nash.claire
3.2 years ago by
nash.claire10 wrote:

Hi everyone,

Sorry to bother all you experts but I have a "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 the Sort module (SAM tools) and this didn't fix the problem. I don't think it is an issue with my files not being co-ordinate sorted as I've managed to use them in Picard.MarkDuplicates in the publicly available GenePattern software suite. I think someone may have had a similar issue with this before and you were trying to sort it. Have you managed to figure it out yet? I'm a little bit stuck with my analysis otherwise!

Thanks in advance

software error samtools bam • 728 views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by nash.claire10
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


One prior issue had to do with the tool form enabling job submission without any filter flags. Please double check that this is not the problem in your case.

The ticket to address that usage issue is here, should you wish to follow it for updates:

If this does not resolve the issue, double check if this problem can be reproduced on (if not already working there). If so, please submit a bug report, being sure to leave all inputs and outputs including the error datasets undeleted. Please place a link to this post in the comments. 

If the tool is not a problem at and you are working somewhere else, please share more details about where you are working. 

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

Hi Jen,

Thanks for getting back to me.

I've been using the main public Galaxy server ( as you say. I think I've managed to find a workaround anyway but I can replicate the problem again and report the bug and see if you can figure out what's going wrong? It's probably something I'm doing as this is my first time trying to analyse ChIP-seq data like this!

ADD REPLYlink written 3.2 years ago by nash.claire10

The issue was the formatting of the filter terms. Aligning to the example on the tool form should resolve the error. Thanks for sending this in! Jen, Galaxy team

ADD REPLYlink written 3.2 years ago by Jennifer Hillman Jackson25k
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