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Question: BAM Tools problem
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gravatar for zarnegar
3.4 years ago by
zarnegar • 0
United States
zarnegar • 0 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 • 1.1k views
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written 3.4 years ago by zarnegar • 0

On which server does this happen? Galaxy main?

ADD REPLY • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

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 REPLY • link written 3.4 years ago by zarnegar • 0

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 REPLY • link written 2.8 years ago by lagoba • 0
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