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NCBI Prokaryotic Genome Annotation Pipeline
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Error with updating pgap #259

Closed stalact closed 1 year ago

stalact commented 1 year ago

Hello, I installed and used pgap some weeks ago as recommended in the Quick Start Section . Now I wanted to update the version, because the warning pops up while executing pgap:

The latest version of PGAP is 2023-05-17.build6771, you are using version 2022-12-13.build6494, please update.

I tried to update with the --update option, but it didn't work out. Deleting the docker image and pgap files, and installing it again installs the version 2022-12-13.build6494 again.

Is there a possibility to update the pgap version to 2023-05-17.build6771?

Thanks and best regards! :-)

azat-badretdin commented 1 year ago

Thank you, user @stalact for your report.

Could you please post what you see on screen?

Thanks!

stalact commented 1 year ago

Thanks for your quick response!

i tried to run the test data:

$ sudo ./pgap.py -r -o mg37_results -g .pgap/test_genomes/MG37/ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasmoides genitalium' The latest version of PGAP is 2023-05-17.build6771, you are using version 2022-12-13.build6494, please update. Output will be placed in: /home/linuxpc/tools/pgap/mg37_results

When I tried to update its downloading the db, but its not used when the program is executed:

$ sudo ./pgap.py --update The latest version of PGAP is 2023-05-17.build6771, you are using version 2022-12-13.build6494, please update. installation directory: /root/.pgap Dateisystem 1K-Blöcke Benutzt Verfügbar Verw% Eingehängt auf /dev/nvme0n1p2 1967392744 325622112 1541758756 18% / Downloading (as needed) Docker image ncbi/pgap:2023-05-17.build6771 Downloading and extracting tarball: https://s3.amazonaws.com/pgap/input-2023-05-17.build6771.tgz 2023-05-17.build6771: Pulling from ncbi/pgap Digest: sha256:6067b42ef74eca02fb754be07c78ca2f40dccb0ca3e48edfe7ec204b2a872ce7 Status: Image is up to date for ncbi/pgap:2023-05-17.build6771 docker.io/ncbi/pgap:2023-05-17.build6771 ^CTraceback (most recent call last):ytes (0.25%)

I terminated the download in that case Hope I could explain the problem a bit better? best regards

azat-badretdin commented 1 year ago

I am not sure why you interrupted the last command, it seems to have been doing the right thing before you interrupted it.

stalact commented 1 year ago

I interrupted it just for the screenshot. I tried the same thing several times, and it somehow worked now! Thanks for your help! :-)