Hi all,

My galaxy is the last update and I work with samtools 1.2.
I have a bug with the sorting and the upload of bam file.
This bug appears only when I try to upload bam sorted by name or when
I try to sort by name.
When I work with bam sorted by coordinate, there is no problem.

So, when I try to sort a bam file by name, this error appears under
the "bug icon" :

Tool execution generated the following error message:
[bam_sort_core] merging from 20 files...
*** Error in `python': double free or corruption (!prev): 0x0000000002897990 ***
Aborted (core dumped)

The tool produced the following additional output:

[E::hts_idx_push] chromosome blocks not continuous
Galaxy attempted to build the BAM index with samtools 1.0+ but failed:
[Errno 2] No such file or directory:
'/data/galaxy-dist/database/job_working_directory/024/24109/__dataset_48619_metadata_temp_file_MqhjBN.bai'

And the same type of error appears when I try to upload bam sorted by name.


What I understand is that the bam can be sorted properly (The command
line to sort is ok in a terminal with no bug and I can follow this
step in the job_working_directory during the run) but Galaxy seems to
fail to create a bai.

For our analysis pipeline, I think the bai is not crucial, is it
possible to avoid this creation of bai during uploading and sorting of
bam file by name ?

Is there another problem than this creation of bai ?

Thanks.

Julie
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