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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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Problem with temporary file handling during mpileup #11

Closed tjakobi closed 8 years ago

tjakobi commented 8 years ago

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 commented 8 years ago

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.