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obenno / ShinySyn

A shiny application to visualize MCscan result
MIT License
33 stars 8 forks source link

FileNotFoundError: [Errno 2] No such file or directory: 'Query.bed' #2

Open jmvega53 opened 2 years ago

jmvega53 commented 2 years ago

Hello, got this error running de MCscan pipeline. I uploaded both .fasta and .gff3 for query and subject. (Pnotatum is the query name) I installed with conda for Linux. Follows the traceback on stdout. The tool looks really nice, would much appreciate using it, tahnk you in advance

Traceback (most recent call last): File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/compara/catalog.py", line 955, in main() File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/compara/catalog.py", line 78, in main p.dispatch(globals()) File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/apps/base.py", line 110, in dispatch globalsaction File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/compara/catalog.py", line 703, in ortholog blastfilter_main(dargs) File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/compara/blastfilter.py", line 322, in main blastfilter_main(blastfile, p, opts) File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/compara/blastfilter.py", line 38, in blastfilter_main qbed, sbed, qorder, sorder, is_self = check_beds(blast_file, p, opts) File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/compara/synteny.py", line 514, in check_beds qbed = Bed(opts.qbed, sorted=sorted) File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/formats/bed.py", line 144, in init for line in must_open(filename): File "/home/juan/anaconda3/envs/shinysyn/lib/python3.9/site-packages/jcvi/formats/base.py", line 433, in must_open fp = open(filename, mode) FileNotFoundError: [Errno 2] No such file or directory: 'Pnotatum.bed'

obenno commented 2 years ago

Hi

Thanks for using ShinySyn, the issue may caused by the format of your GFF3. Can you share your input fasta and gff3?

Bests, Zhixia