search

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
Other
294 stars 89 forks source link

[BUG] A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments #294

Closed TCHeaven closed 3 months ago

TCHeaven commented 4 months ago

Describe the bug I am trying to run the test data without internet access however, I receive the error: 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 -g/--genome arguments replace the YAML file argument input.

To Reproduce I am runnign the python3 ~/pgap.py --debug --no-internet --no-self-update --docker singularity --container-path ~/pgap_2023-10-03.build7061.sif -r -o mg37_results -g ~/.pgap/test_genomes/MG37/ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasmoides genitalium'

Expected behavior Results outputted to a mg37_results subdirectory

Software versions (please complete the following information):

Log Files no log files are produced

azat-badretdin commented 4 months ago

Thank you for your report, Thomas!

I presume you installed PGAP someone on accessible network path before running this command?

Is your pgap.py up to date?

TCHeaven commented 4 months ago

pgap.py was downloaded sometime last week via curl -OL https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py and so should be up to date

azat-badretdin commented 4 months ago

Do you have a setup WITH internet? Does it work there?

TCHeaven commented 4 months ago

No, the programs cannot be run on an internet connected node

azat-badretdin commented 4 months ago

Thanks. We will try to reproduce it on our singularity-equipped instance.

TCHeaven commented 4 months ago

FYI. If I remove the -s and -g flags it seems that the program is still looking for docker despite the --docker singularity setting.

Running: python3 ~/pgap.py --debug --no-internet --docker singularity --container-path ~/pgap_2023-10-03.build7061.sif -r -o mg37_results

Results in: --no-internet flag enabled, not checking remote versions. Docker not found.

azat-badretdin commented 4 months ago

If I remove the -s and -g flags

It will mean that you are not supplying any input.

Then at the absence of user input the script will go into software update/download/upgrade mode depending on parameters. Given no internet flag this will become no-can-do.

azat-badretdin commented 3 months ago

I reopened our permanent-singularity awspet, install latest pgap, created .sif file and ran the command provided, everything works.

 ~/pgap.py --debug --no-internet --no-self-update --docker singularity --container-path ~/pgap_2023-10-03.build7061.sif -r -o mg37_results -g ~/.pgap/test_genomes/MG37/ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasmoides genitalium'