pgap

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Error: Final process status is permanentFail

13

Hi, I am following my previous issue #304, it has been closed. I am already using 'salmonella' in submol.yaml, but I am not able to get the results. When I...

sekhwal

Get_Proteins_app issues

13

./pgap.py -n -o out_directory -g sequence.fasta -s Staphylococcus [cwltool.log](https://github.com/ncbi/pgap/files/15212092/cwltool.log) I don't know what the problem is anymore, the last version worked fine

asd1864714

Update pgap.py

2

Converted problematic strings to raw strings to avoid syntax warnings with Python 3.12+

iskold

[BUG] Fail in GenBank output file

8

Why does pgap does not give me the GenBank (.gb) file in the output?

juansebe1

[BUG] Binding non-existent file

8

**Describe the bug** PGAP fails to start a singularity container because it is attempting to bind a file that does not yet exist. **To Reproduce** Using PGAP version 2023-10-03.build7061. Followed...

kkrick-sdsu

[BUG] When two input genomes have same basename, the first genome is mistakenly used for the second run.

3

**Describe the bug** When two input genomes have same basename, the genome from the first run is mistakenly used for the second run. The cause is that for the first...

pvstodghill

[BUG] SIGBUS error on HPC using singularity

9

Hello, I'm trying to run PGAP on an HPC cluster using singularity + slurm and I'm running into some troubles. While pgap is installing/running fine with our "test genome" on...

AdrianZrm

[FEATURE REQUEST] Expected output of test_genomes?

1

**Is your feature request related to a problem? Please describe.** I ran PGAP on the test genome (test_genomes-2022-12-13.build6494 MG37), but how do I check if the run behaviour was as...

lxsteiner

[BUG] GFF3 output file does not contain sequence-region name

2

**Describe the bug** The .gff (GFF3) output of the PGAP pipeline produces GFF3 files that do not contain the name of the sequence-region on the ##sequence-region line. This hurts downstream...

watsonar

[BUG] A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments. The -s/--organism and the -g/--genome arguments replace the YAML file argument input.

4

The bug is: pgap.py: error: Invalid Command Line Argument Error: A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments. The -s/--organism and the...

yulinpengcool