Question: BAM Tools problem
0
gravatar for zarnegar
3.1 years ago by
zarnegar0
United States
zarnegar0 wrote:

When I attempt to merge BAM files I receive the following:

[bam_index_core] the alignment is not sorted (NS500126:311:HFGKHBGXX:4:21604:15061:18811): 3000920 > 3000506 in 1-th chr [bam_index_build2] fail to index the BAM file. *** glibc detected *** python: double free or corruption (!prev): 0x0000000003687440

 

If I load my BAMs into Cistrome Galaxy, the SAMtools BAM merge works just fine.  What is going on?

software error • 921 views
ADD COMMENTlink written 3.1 years ago by zarnegar0

On which server does this happen? Galaxy main?

ADD REPLYlink written 3.1 years ago by Bjoern Gruening5.1k

The default, Galaxy Main I assume.  I did not see an option to run the job on a specified server (I have only noticed server choice options when mapping reads).

 

 

ADD REPLYlink written 3.1 years ago by zarnegar0

Hello,

Was this problem ever solved? I am getting a very similar error message from samtools_sort on a local Galaxy instance:

*** Error in `python': double free or corruption (!prev): 0x000000000231ebd0 ***
Aborted (core dumped)
[bam_sort_core] merging from 33 files...
[bam_index_core] the alignment is not sorted (HISEQ:436:C85CBANXX:2:1101:1001:13586): 21649621 > 21637178 in 15-th chr
[bam_index_build2] fail to index the BAM file.

Any help is greatly appreciated! 

ADD REPLYlink written 2.4 years ago by lagoba0
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