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YangLab / CIRCexplorer2

circular RNA analysis toolset
http://circexplorer2.readthedocs.org/
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ValueError: need more than 2 values to unpack #39

Closed lliaokc closed 4 years ago

lliaokc commented 4 years ago

Hi,

I am running CIRCexplorer2 with the following commands [use CIRCexplorer2 parse to obtain back_spliced_junction.bed from STAR generated Chimeric.out.junction] :

CIRCexplorer2 annotate -r genome.gtf -g genome.fasta -b back_spliced_junction.bed -o outfiles

Then, I have the following error messages:

Start to annotate fusion junctions... Traceback (most recent call last): File "/usr/local/bin/CIRCexplorer2", line 9, in load_entry_point('CIRCexplorer2==2.3.8', 'console_scripts', 'CIRCexplorer2')() File "build/bdist.linux-x86_64/egg/circ2/command_parse.py", line 51, in main File "build/bdist.linux-x86_64/egg/circ2/helper.py", line 38, in wrapper File "build/bdist.linux-x86_64/egg/circ2/annotate.py", line 38, in annotate return attrs[key] File "build/bdist.linux-x86_64/egg/circ2/annotate.py", line 50, in annotate_fusion return get_name File "build/bdist.linux-x86_64/egg/circ2/parser.py", line 76, in parse_ref ValueError: need more than 2 values to unpack

Could you please provide any suggestions to solve this problem? Thanks.

kepbod commented 4 years ago

CIRCexplorer2 annotate did not accept the gtf file. Please use the correct format for gene annotation file (https://circexplorer2.readthedocs.io/en/latest/modules/annotate/).