csamtools crash when running a gatk-variant project

[brainstorm]

Hi @chapmanb, @roryk,

I'm setting the pipeline in our HPC cluster, using the test data as input files:

bcbio_nextgen.py -w template gatk-variant project1 tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_1_fastq.txt tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_2_fastq.txt

cd ~/roman/dev/bcbio-nextgen/project1/work

bcbio_nextgen.py ~/config/bcbio_system.yaml ~/roman/dev/bcbio-nextgen/project1/config/project1.yaml

But pysam is not very happy about the header(s) of the test bam file:

(...)
  File "~/roman/.virtualenvs/bcbio/lib/python2.7/site-packages/bcbio_nextgen-0.7.0a-py2.7.egg/bcbio/pipeline/shared.py", line 51, in _do_work
    with closing(pysam.Samfile(bam_file, "rb")) as work_bam:
  File "csamtools.pyx", line 597, in csamtools.Samfile.__cinit__ (pysam/csamtools.c:5982)
  File "csamtools.pyx", line 760, in csamtools.Samfile._open (pysam/csamtools.c:7675)
ValueError: file header is empty (mode='rb') - is it SAM/BAM format?

Are those headers critical for the rest of the pipeline to go on smoothly?

Cheers!
Roman

@guillermo-carrasco

[brainstorm]

Actually, it crashes while running in the same way while running nosetests -v -s too.

[chapmanb]

Roman;
There appears to be something wrong with the initial output file from alignment. For the automated tests, can you look at the file in align/Test1/7_100326_FC6107FAAXX-sort.bam and see what it looks like? If you look further up in the log messages I'd guess that there is another error message that might have more insight into the issue.

[brainstorm]

Thanks Brad!

Looking closer I stumbled upon this one:

[2013-07-22 15:40]  bwa mem alignment from BAM: Test1
[2013-07-22 15:40]  [main] unrecognized command 'mem'
[2013-07-22 15:40]  [samopen] no @SQ lines in the header.

Changed from bwa/0.6.2 to bwa/0.7.4 and back on track :)

Cheers!
Roman