Question: python: double free or corruption -
gravatar for inspiresnehal
2.8 years ago by
inspiresnehal20 wrote:

I am running below command in loop for multiple datasets. If I just run one time. it runs fine. But if I run 2 or more times then it gives below error:

Command is :

bowtie2 -q -x /home/sn/Galaxy/hg19/bowtie_path/base/genome -U $input | samtools view -bS -> subdir3/$output
samtools sort subdir3/$output subdir3/$output_prefix


Error is :

[bam_index_core] the alignment is not sorted (SRR1686705.4731497): 22-th chr > 8-th chr
[bam_index_build2] fail to index the BAM file.
*** glibc detected *** python: double free or corruption (out): 0x00007fc4b03fa990 ***

This error doesn't occur if I run the same command on the command line:

Is there any parameter in the Galaxy which needs to be adjusted for the job to run for memory intensive jobs?



galaxy samtools • 1.2k views
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