Comments (3)
Thank you for your report, user @namho4577 !
Your command line says:
./pgap.py -r -o E_coli_result9 -g $HOME/.pgap/test_genomes/MG37/input.yaml -s 'Escherichia coli' --ignore-all-errors
When you are using -g
option it requires a FASTA file, not a YAML file.
from pgap.
from pgap.
If you would like to continue using YAML file replace -s and -g parameters with YAML file.
So this:
./pgap.py -r -o E_coli_result9 -g $HOME/.pgap/test_genomes/MG37/input.yaml -s 'Escherichia coli' --ignore-all-errors
will become this
./pgap.py -r --ignore-all-errors -o E_coli_result9 $HOME/.pgap/test_genomes/MG37/input.yaml
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Related Issues (20)
- [BUG] A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments HOT 8
- [BUG] -c flag not received: /mnt/shared/scratch/theaven/uncompressed/hogenhout/pgap-s7 HOT 1
- [BUG] Fail in GenBank output file HOT 9
- product protein name issues HOT 3
- [BUG] Final process status is permanentFail HOT 1
- [Error] Docker exited with rc =1 HOT 2
- Get_Proteins_app issues HOT 14
- Error: Final process status is permanentFail HOT 7
- Error: Final process status is permanentFail HOT 17
- source code for gc_get_molecules HOT 2
- PGAP for multiple users HOT 2
- ORF prediction issue HOT 3
- [BUG] Genus species requirement HOT 8
- [BUG] PGAP fails on test genome when PGAP_INPUT_DIR set to other than default HOT 4
- Species_Requirement_option HOT 1
- [BUG] Failing to run some sequences HOT 2
- [BUG] FATAL: "cwltool": executable file not found in $PATH in 2024-04-27.build7426 HOT 4
- [BUG] GFF3 output file does not contain sequence-region name HOT 3
- [BUG] PGAP failed, docker exited with rc = 1 HOT 11
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