[BUG] <title>How to run pgap.py with qsub file.

[wurunbiao162]

Describe the bug Error running pgap in clustered server.

**Running script $ qsub works.sh The following commands are included in the works.sh file.

!/bin/sh

#PBS -N lucky
#PBS -l nodes=1:ppn=10
#PBS -q blade
#PBS -l walltime=1000:00:00
#PBS -d /public1/home/20240101_Bacteria_Genome 
#PBS -j oe

python3 ~/soft/pgap.py  -r -o mg37_results -g ~/.pgap/test_genomes-2023-10- 

03.build7061/MG37/ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasmoides genitaliu' --no-self-update --no-internet .

Log Files [2024-01-19 19:14:40][INFO][157337.admin] ######################## Job 157337.admin start to execute pre.sh! ########################## [2024-01-19 19:14:40][INFO][157337.admin] Goldenable & storageenable both are false, job ran without making reserve! Fri Jan 19 19:13:29 CST 2024 --no-internet flag enabled, not checking remote versions. Docker not found.

Software versions (please complete the following information):

• OS: [ CentOS 7]
• pgap.py --version, or docker image version. [2023-10-03.build7061]
• Docker version. [Docker version 24.0.7, build afdd53b]

Additional context Would you like to provide the detail commands to run pgap pipeline.

[azat-badretdin]

Thank you for your report, user @wurunbiao162 !

It says: Docker not found. Do you have docker hooked up on your cluster machines?

[wurunbiao162]

I have installed docker and pulling pgap.

(base) [jian@login ~]$ docker images REPOSITORY TAG IMAGE ID CREATED SIZE docker.io/ncbi/pgap-utils 2023-10-03.build7061 cbaed0b6edfb 3 months ago 11.9 GB

[azat-badretdin]

• Did you run this command on one of the cluster machines?
• The docker image you listed is not the image that is used by pgap.py is the listing complete? Did you use ./pgap.py to install as in Quick Notes?

[wurunbiao162]

Thank you azat， I also run the ./pgap.py --update，get the files /public1/home/jian/.pgap/input-2023-10-03.build7061, test_genomes-2023-10-03.build7061.

[azat-badretdin]

Thanks. Note that the propagation of this installation to the computational server and accessibility of data and docker image from that server is in the hands of the user, NCBI does not support such thing. That's why I ask which server did you use to check your docker status.