[BUG] Problem with Ani-taxcheck. Warning Final process status is permanentFail.

[MicoNick]

Good afternoon, dear PGAP support representatives. I am experiencing a problem with using PGAP. I did not have this issue with the 5508 version. I will try to describe it briefly.

Before PGAP was updated to version 5508, the Ani-tax check was always normal and completed the subsequent genome annotation without any errors. Starting with version 5742 and installing the new version 5872 today, the error did not go away: the ani-tax checker ends with a permanent error (in my opinion, related to the absence of a number of files in the input folder). In the folder of version 5508 there were files such as: ANI_cutoff, ani-report, gcextract2, kmer.sqlite, kmer_uri_list, taxsynon which are missing in the 5742 and 5872 folders.

The issue occurs not only with our own genomes, but also with test genomes. Tried to do the ani check on the MG37 test genome. The issue is the same. Logs and all other folders of the executed command with the debug flag attached to this post.

Can you please tell me what is the reason and what I can do to make this function work again in PGAP?

Software versions:

• OS: Linux mint 20.2
• pgap.py --version 5742, 5872
• Docker version is the same as pgap itself

debug_and_cwltool_log.zip

[azat-badretdin]

Thank you for your report, user MicoNick!

Could you please post the result of the command find . -name input-2022-02-10.build5872 -type d | ls -ltrR? Thanks

[MicoNick]

Yes, sure! As I understand in your code there is a mistake and instead of version 3625 it should be 5872, right?

I put the result in txt file, which is in the archive.

Thank you for the wait, the workstation is far away from me and only now was I able to execute the command. find_results.zip

[azat-badretdin]

Thanks,

Please run ./pgap.py --update --taxcheck to be able to run your genomes with --taxcheck option

[MicoNick]

In response to this command, the terminal outputs: PGAP version 2022-02-10. build5872 is up to date.

However, the --taxcheck was never run.

[MicoNick]

In response to this command, the terminal outputs: PGAP version 2022-02-10. build5872 is up to date.

However, the --taxcheck was never run. And every time crash with permanent fail.

пт, 18 февр. 2022 г. в 12:50, Azat Badretdin @.***>:

Thanks,

Please run ./pgap.py --update --taxcheck to be able to run your genomes with --taxcheck option

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[azat-badretdin]

Could you please do it from the fresh directory?

[MicoNick]

Could you please do it from the fresh directory?

Not from the home directory, where is pgap itself located?

[azat-badretdin]

Basically, you need to start fresh, unfortunately we do not have incremental update that can just add missing taxcheck reference data to existing pgap reference data. Sorry about that.

[MicoNick]

He started a new database download process. No problem! Many thanks for help! Hope this helps solve my problem. After completing the download, can I transfer these directories along with the script without problems to another location for my convenience?

[azat-badretdin]

Sure, just keep the relative paths the same.

[MicoNick]

Sure, just keep the relative paths the same.

Ok! Many thanks! After all the downloads and attempts to launch I will write again.

[MicoNick]

Dear Azat! Many thanks for your help. Now, PGAP work very well.

[azat-badretdin]

You are very welcome! Thank you for choosing PGAP for your genomic annotation needs!

[azat-badretdin]

Looks like you might have been affected with the bug we introduced accidentally in the last release. It is fixed now. Now you should not be worried with manually downloading modules as an extra step, the script will do it for y ou automatically as it should be.