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

[jmvega53]

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]

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