tmp_DCC files didn't get combine to generate 4 output files

[sambhav2mishra]

Describe the bug
tmp_DCC files didn't get combine to generate 4 output files i.e CircRNAcount, CircCoordinates, CircSkipJunctions and LinearCount

Command line used for the command

circtools detect @samplesheet -mt1 @mate1 -mt2 @mate2 -D -R Final_repeats.gtf -an gencode.v30.annotation.gtf -Pi -F -M -Nr 5 6 -fg -G -A GRCh38_gencode.fa

2. Complete error message

Screenshots

Desktop (please complete the following information):

• OS: [ Ubuntu 18.04]
• Python version [Python 2.7.15rc1]

[tjakobi]

Hi @sambhav2mishra ,

did you try to set the filtering threshold lower, i.e. -Nr 2 2 for example? The warning message just states that no circles have been found which is most probably due to to stringent filtering.

Cheers,
Tobias

[sambhav2mishra]

Thanks Tobias it helped me with filtering but it gave another problem:

File "/home/dranshuman/.local/bin/DCC", line 11, in
load_entry_point('DCC==0.4.7', 'console_scripts', 'DCC')()
File "build/bdist.linux-x86_64/egg/DCC/main.py", line 364, in main
File "build/bdist.linux-x86_64/egg/DCC/circFilter.py", line 92, in filter_nonrep
File "build/bdist.linux-x86_64/egg/DCC/circFilter.py", line 85, in read_rep_region
File "/home/dranshuman/.local/lib/python2.7/site-packages/HTSeq-0.11.2-py2.7-linux-x86_64.egg/HTSeq/init.py", line 207, in iter
strand, frame, attributeStr) = line.split("\t", 8)
ValueError: need more than 1 value to unpack

[tjakobi]

Hi @sambhav2mishra,

could you please paste the first lines of your repeat annotation file?

head Final_repeats.gtf

Cheers,
Tobias

[sambhav2mishra]

Hello Tobias
although you recommended to choose RepeatMasker together with Simple Repeats and combine the results afterwards but i have created my gtf file using only repeatMasker and i have attached a file consisting of few lines of annotation file.
gtf.txt