samtools errors caused by mapping.py

[koppk]

Hi all,

changing these two lines in mapping.py seems to prevent an error thrown by samtools which made IVA runs exit.

old:

    #sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix

new:

    sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' -o' + final_bam

old:

    #index_cmd = 'samtools index ' + out_prefix + '.bam'

new:

    index_cmd = 'samtools index ' + final_bam

Cheers, Katharina

[martinghunt]

Hi Katharina,

What version of samtools are you using? It's on the to-do list to support 1.3 (see issue #57).

Thanks, Martin

[koppk]

Hi Martin, it's samtools Beta Release 1.3 (15 December 2015)

I found this in the file NEWS of that release:
Noteworthy changes in samtools:
* The obsolete "samtools sort in.bam out.prefix" usage has been removed.
  If you are still using -f, -o, or out.prefix, convert to use -T PREFIX
  and/or -o FILE instead.  (#295, #349, #356, #418, PR #441; see also
  discussions in #171, #213.)
It seems with the above mentioned changes in mapping.py, though.
I really appreciate having discovered IVA, as I am trying to assemble NGS runs from "very difficult" metagenomics samples (low concentration, probably partially degraded viral RNA, dominating host mRNA ...) and so far IVA worked best ... 
Thanks,
Katharina 

[martinghunt]

Hi Katharina,

Yes, the plan is to support samtools 1.3, but keep support for older versions as well (that don't have the -o option), so it's a little more work than just changing those two lines.

Glad it's working well!

Thanks, Martin

[martinghunt]

This is now fixed in the new version 1.0.5, whcih supports the new and old samtools. Thanks @satta.