PGAP error

[0123615177]

Hi

1) I am having trouble with getting PGAP running.

Firstly, I did the installation of docker desktop. https://docs.docker.com/desktop/install/ubuntu/

Docker is located in the following directory; /bin/docker

2) After this, I installed the 3 things needed for PGAP, namely (docker image, the supplementary reference files, CWL code) from: https://github.com/ncbi/pgap/wiki/Installation (using the latest version 2022-12-13)

I got pgap.py with th folowing commands

$ wget https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py $ chmod +x pgap.py $ ./pgap.py --update

All things related to PGAP are in the directory /home/margot:

After the PGAP downloads and installation, the docker contains the following images

So in my wd I also have the files for analysis, namely the genome .fasta file (Thermobofoda.fna), and the two .yaml files: Thermobifida_alba.yaml and Thermobifida_alba_meta.yaml

Here is what the content looks like: Thermobifida_alba.yaml: Thermobifida_alba_meta.yaml:

So after opening docker, I run the following command from my wd: ./pgap.py -r -o Results Thermobifida_alba.yaml

But then I get the following error message: PGAP version 2022-12-13.build6494 is up to date. Output will be placed in: /home/margot/Results WARNING: memory (GiB) is less than the recommended value of 8 WARNING: memory per CPU core (GiB) is less than the recommended value of 2 PGAP failed, docker exited with rc = 125 Unable to find error in log file.

PS. would also like to mention that the 'File sharing' of docker path is set to my wd: /home/margot

I have tried many things, but I do not know how to fix this. Can you please suggest somthing? Thanks so much Margot

[0123615177]

hi

this is what is in the directory after it has run and given the error:

[azat-badretdin]

Thanks. How about ls -l?

[0123615177]

hi Here it is:

[azat-badretdin]

Thanks. Could you please do this test:

/usr/local/bin/docker run -i --rm --user 1000:1000 \
--volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z \
--volume /home/margot:/pgap/user_input:z \
--volume /home/margot/mytmp:/tmp:rw,z \
--volume /home/margot/Results:/pgap/output:rw,z \
ncbi/pgap:2022-12-13.build6494  \
whoami

Thanks

[0123615177]

Hi:

(base) margot@margot-B365M-DS3H:/$ /usr/local/bin/docker run -i --rm --user 1000:1000 --volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z --volume /home/margot:/pgap/user_input:z --volume /home/margot/mytmp:/tmp:rw,z --volume /home/margot/Results:/pgap/output:rw,z ncbi/pgap:2022-12-13.build6494 whoami "docker run" requires at least 1 argument. See 'docker run --help'.

Usage: docker run [OPTIONS] IMAGE [COMMAND] [ARG...]

Create and run a new container from an image --volume: command not found --volume: command not found --volume: command not found --volume: command not found bash: ncbi/pgap:2022-12-13.build6494: No such file or directory margot

[azat-badretdin]

Thanks. Could you please do this test:

/usr/local/bin/docker run -i --rm --user 1000:1000 \
--volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z \
--volume /home/margot:/pgap/user_input:z \
--volume /home/margot/mytmp:/tmp:rw,z \
--volume /home/margot/Results:/pgap/output:rw,z \
ncbi/pgap:2022-12-13.build6494  \
whoami

Thanks

[0123615177]

Hi: (base) margot@margot-B365M-DS3H:~$ /usr/local/bin/docker run -i --rm --user 1000:1000 \ --volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z \ --volume /home/margot:/pgap/user_input:z \ --volume /home/margot/mytmp:/tmp:rw,z \ --volume /home/margot/Results:/pgap/output:rw,z \ ncbi/pgap:2022-12-13.build6494 \ whoami gpipe (base) margot@margot-B365M-DS3H:~$

BUT i click on the docker icon/app before i run the script so that it opens. I also do this before I run PGAP:

[adriangeerre]

Hi, Thanks for a long and meticulous post. I would like to say that I am currently facing this same issue too. I have a pipeline which used to work perfectly (implemented 6-8 months ago) but nowadays it stops the annotations with the error "WARNING Final process status is permanentFail".

I have tested the installation in 2 different systems, HPC and laptop, using Singularity and Docker with the MG37 test input and it would:

• Fail inmediately with error rc = 1 or rc = 125
• Complain always about "tmp disk space" even after defining $TMPDIR, even when the tmp has more than 10GB free storage.
• If I manage to make it run, the execution will finish abruptly and reporting "permanentFail".

Let me know if I can help. Best regards

[azat-badretdin]

Thank you for your comment @adriangeerre could you please open a separate ticket? Please post part of the cwltool.log that precedes first permanentFail message.