It would be very cool to support compressed bins in bindir folder. If I specify suffix fa.gz - it fails (I guess because it tries to open uncompressed file)
eukcc folder --improve_percent 10 --n_combine 1 --threads 16 --improve_ratio 5 --links metabat2.links.csv --min_links 100 --suffix .fa.gz --db eukcc2_db_ver_1.1 --out metabat2_merged_bins --prefix "metabat2_merged." maxbin
error
Command error:
22-08-2023 13:35:49: EukCC version 2.1.2
22-08-2023 13:35:49: Found 4 bins
Traceback (most recent call last):
File "/opt/conda/bin/eukcc", line 8, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.8/site-packages/eukcc/__main__.py", line 497, in main
eukcc_folder(args)
File "/opt/conda/lib/python3.8/site-packages/eukcc/refine.py", line 65, in eukcc_folder
refine(state)
File "/opt/conda/lib/python3.8/site-packages/eukcc/refine.py", line 136, in refine
state["contigs"] = merge_fasta(
File "/opt/conda/lib/python3.8/site-packages/eukcc/fasta.py", line 48, in merge_fasta
for seq in Fasta(fasta):
File "/opt/conda/lib/python3.8/site-packages/eukcc/fasta.py", line 94, in Fasta
raise ValueError("The provided fasta file is malformed: {}".format(path))
ValueError: The provided fasta file is malformed: maxbin/MaxBin2.001.fa.gz
It would be very cool to support compressed bins in bindir folder. If I specify suffix fa.gz - it fails (I guess because it tries to open uncompressed file)
eukcc folder --improve_percent 10 --n_combine 1 --threads 16 --improve_ratio 5 --links metabat2.links.csv --min_links 100 --suffix .fa.gz --db eukcc2_db_ver_1.1 --out metabat2_merged_bins --prefix "metabat2_merged." maxbin
error