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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
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FileNotFoundError: Could not find fasta file #35

Open alienn233 opened 1 year ago

alienn233 commented 1 year ago

coomand : docker run -it quay.io/microbiome-informatics/eukcc single --out outfolder --threads 8 --db ~/software/eukccdb/eukcc2_db_ver_1.1 ~/software/eukccdb/EukCC-master/tests/testfiles/N50_1.fa

err:: Traceback (most recent call last): File "/opt/conda/bin/eukcc", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/eukcc/main.py", line 495, in main run_eukcc(args) File "/opt/conda/lib/python3.8/site-packages/eukcc/main.py", line 57, in run_eukcc state["seqtype"] = determine_type(state["fasta"]) File "/opt/conda/lib/python3.8/site-packages/eukcc/fasta.py", line 27, in determine_type for record in fa: File "/opt/conda/lib/python3.8/site-packages/eukcc/fasta.py", line 93, in Fasta if validate_fasta(path) is False: File "/opt/conda/lib/python3.8/site-packages/eukcc/fasta.py", line 135, in validate_fasta raise FileNotFoundError("Could not find fasta file") FileNotFoundError: Could not find fasta file

But i already had fasta file

openpaul commented 1 year ago

Your homefolder might not be mounted in the docker container? The fasta file is not reachable for eukcc. This should not be a bug in EukCC but likely is just some permission/docker issue