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Problem with temporary file handling during mpileup #11

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tjakobi opened this issue Jul 11, 2016 · 1 comment
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Problem with temporary file handling during mpileup #11

tjakobi opened this issue Jul 11, 2016 · 1 comment
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tjakobi commented Jul 11, 2016

Error seems to occur during linear gene expression counting step:

Started linear gene expression counting for 7EN2.pairedAligned.out.bam => running mpileup for start positions [7EN2.pairedAligned.out.bam] return self.map_async(func, iterable, chunksize).get() File "/ibios/tbi_cluster/11.4/x86_64/python/python-2.7.2/lib/python2.7/multiprocessing/pool.py", line 522, in get raise self._value IOError: [Errno 2] No such file or directory: '_tmp_DCC/tmp_/AK173.pairedAligned.out.bam_YF5U7D_junction.linear'
@tjakobi tjakobi self-assigned this Jul 11, 2016
@tjakobi tjakobi added the bug label Jul 11, 2016
tjakobi added a commit that referenced this issue Jul 14, 2016
@tjakobi
Fixes issue #10.
779bc2c 
The 'CircCoordinate' file now again has a proper column headers:
Issue #11, dealing with the slightly different annotations still needs to be resolved.
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tjakobi commented Jul 19, 2016

The issue arises when relative or absolute file locations are supplied to DCC. The temporary file name creation does not handle the removal of the path to the file.

tjakobi added a commit that referenced this issue Jul 19, 2016
@tjakobi
Fixes #11.
4c0181d 
File names from from samplesheet an mate files were used as template for temporary files without stripping possible relative or absolute paths. This error has been corrected, os.path.basename(path) now sanitizes the supplied file names.
@tjakobi tjakobi closed this as completed Jul 19, 2016
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