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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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IOError: [Errno 2] No such file or directory: CircRNACount #66

Closed MaxHills closed 5 years ago

MaxHills commented 5 years ago

CircRNACount is supposed to be output by DCC, but I receive an error that it does not exist a few seconds after running DCC from the command line.

  1. Command line used for the command

DCC \ @dcc_fileLists/ADAR_samplesheet \ -B @dcc_fileLists/ADAR_BAM_fileList \ -an $home/mm10/mm10.all.gtf \ -T 14 \ -M \ -Nr 2 4 \ -G \ -A $home/mm10/mm10.ucsc.fa \ -R $home/mm10/mm10.allRepeats.gtf \ -O dcc/ADAR/

  1. Complete error message

Traceback (most recent call last): File "/home/mh2354/.local/bin/DCC", line 9, in load_entry_point('DCC==0.4.7', 'console_scripts', 'DCC')() File "build/bdist.linux-x86_64/egg/DCC/main.py", line 452, in main File "/n/apps/CentOS7/install/pyenv-1.0.0/pyenv/versions/2.7.5/lib/python2.7/multiprocessing/pool.py", line 250, in map return self.map_async(func, iterable, chunksize).get() File "/n/apps/CentOS7/install/pyenv-1.0.0/pyenv/versions/2.7.5/lib/python2.7/multiprocessing/pool.py", line 554, in get raise self._value IOError: [Errno 2] No such file or directory: 'dcc/ADAR/CircRNACount'

My @samplesheet: cat ADAR_samplesheet /l/Yu/YuLab/Bioinformatics/projects/mhh_CIRCexplorer2/align/starOUT/ADAR/ACTTGA/ACTTGA.Chimeric.out.junction /l/Yu/YuLab/Bioinformatics/projects/mhh_CIRCexplorer2/align/starOUT/ADAR/CAGATC/CAGATC.Chimeric.out.junction /l/Yu/YuLab/Bioinformatics/projects/mhh_CIRCexplorer2/align/starOUT/ADAR/CCGTCC/CCGTCC.Chimeric.out.junction /l/Yu/YuLab/Bioinformatics/projects/mhh_CIRCexplorer2/align/starOUT/ADAR/GCCAAT/GCCAAT.Chimeric.out.junction

My @bam: cat ADAR_BAM_fileList /l/Yu/YuLab/Bioinformatics/projects/mhh_CIRCexplorer2/align/starOUT/ADAR/ACTTGA/ACTTGA.Aligned.sortedByCoord.out.bam /l/Yu/YuLab/Bioinformatics/projects/mhh_CIRCexplorer2/align/starOUT/ADAR/CAGATC/CAGATC.Aligned.sortedByCoord.out.bam /l/Yu/YuLab/Bioinformatics/projects/mhh_CIRCexplorer2/align/starOUT/ADAR/CCGTCC/CCGTCC.Aligned.sortedByCoord.out.bam /l/Yu/YuLab/Bioinformatics/projects/mhh_CIRCexplorer2/align/starOUT/ADAR/GCCAAT/GCCAAT.Aligned.sortedByCoord.out.bam

tjakobi commented 5 years ago

Hi @MaxHills,

you need to specify the -D flag to actually do the circRNA detection (and get the corresponding output file).

I, on the other hand, need to make sure to check for this combination of CLI flags.

Cheers Tobias