Closed a18958 closed 3 years ago
linzhi2013
commented
3 years ago Sorry, I can't determine what's going on there, probably due to problems with installation. Maybe you could try Docker MitoZ-v2.3, or Udocker version which doesn't need sudo privileges.
a18958
commented
3 years ago Sorry for my late reply, it works well in the Docker, thank you! Cheers!
linzhi2013
commented
3 years ago That's great!
Hi, I ran the test file at all2 Module, it seems like can't create the ZZZ_mitoscaf.fa.gbf. Here is the code: `Traceback (most recent call last): File "/public/home/zhangxiuyue/tools/MitoZ/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 238, in
main()
File "/public/home/zhangxiuyue/tools/MitoZ/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 202, in main
seqid_len_topology_relatedSP = get_seq_topology_and_related_sp(gbfile=gbfile, closely_related_sp_file=closely_related_sp_file)
File "/public/home/zhangxiuyue/tools/MitoZ/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py", line 173, in get_seq_topology_and_related_sp
for rec in SeqIO.parse(gbfile, 'gb'):
File "/public/home/zhangxiuyue/anaconda3/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 607, in parse
return iterator_generator(handle)
File "/public/home/zhangxiuyue/anaconda3/lib/python3.6/site-packages/Bio/SeqIO/InsdcIO.py", line 93, in init
super().init(source, mode="t", fmt="GenBank")
File "/public/home/zhangxiuyue/anaconda3/lib/python3.6/site-packages/Bio/SeqIO/Interfaces.py", line 47, in init
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: 'test_mitoscaf.fa.gbf' Error occured when running command: /public/home/zhangxiuyue/anaconda3/bin/python3 /public/home/zhangxiuyue/tools/MitoZ/version_2.3/release_MitoZ_v2.3/bin/common/genbank_gene_stat_v2.py test_mitoscaf.fa.gbf test.most_related_species.txt all2 > summary.txt `