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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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cant find 'tmp_unsortedNoChrM' #33

Closed FranziMe closed 7 years ago

FranziMe commented 7 years ago

Hi, I am running DCC on an organism without an annotated mitochondrial chromosome. It does not matter if I run DCC with -M or not, it also breaks with -k and not, as well as -t and without. I tried various combinations of the flags and I always get the same error:

Traceback (most recent call last): File "/beegfs/group_dv/home/FMetge/home/circRNA/DCC/version.0.4.4/DCC-0.4.4/DCC/main.py", line 782, in <module> main() File "/beegfs/group_dv/home/FMetge/home/circRNA/DCC/version.0.4.4/DCC-0.4.4/DCC/main.py", line 356, in main options.tmp_dir + "tmp_unsortedNoChrM") OSError: [Errno 2] No such file or directory Here are the versions of the python packages I am using

numpy.version '1.9.2' pysam.version '0.9.1' pybedtools.version '0.6.9'

Do you have any recommendations how to fix this?

slurm-365873.txt DCC-2016-10-07_11-05.txt

tjakobi commented 7 years ago

Problem occurs when no -R (repetitive region file) is not supplied. In this case the file tmp_unsortedWithChrM is never created, therefore the following steps are failing regardless of the -M or any other flags.

tjakobi commented 7 years ago

-F has also to be specified, of course. Without -F none of the filtering flags is used at all.