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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.

Home Page:https://dieterichlab.org/software/

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

MaxHills opened this issue · comments

commented

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

commented

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