ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
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[BUG] <title>PGAP failed #316

Closed StickHu closed 1 month ago

StickHu commented 2 months ago

Hi, recently when I was using the PGAP, a problem occurred.

Describe the bug

/data/workdir/huwa/annotation/PGAP/pgap/scripts/./pgap.py:133: SyntaxWarning: invalid escape sequence '[' r = "^[(?P

My command line is "./pgap.py -g /data/workdir/huwa/oral_DB/allspeciesFastq/assembly_dealed/Porphyromonas_gingivalis_fastq/raw_spades/all_checkm_bins/ERR5385081_bin_52.fa -s 'Porphyromonas gingivalis' -r --no-self-update"

Could you please help me solve that? Thanks for your reply.

azat-badretdin commented 2 months ago

Thank you for your report, user @StickHu !

The error you posted might be a transient Internet issue. Could you please retry?

It looks like you have a rigorous Python execution setting that elucidated number of warnings in our Python code that are worth fixing. Thank you for that too!

StickHu commented 2 months ago

Thanks for your reply. However, I have retried several times. Could you please help me fix that?

azat-badretdin commented 2 months ago

Thanks. That must be some systemic Internet problem in a way you set up things. Could you please post your command line?

StickHu commented 2 months ago

Here is my command line "./pgap.py -g /data/workdir/huwa/oral_DB/allspeciesFastq/assembly_dealed/Porphyromonas_gingivalis_fastq/raw_spades/all_checkm_bins/ERR5385081_bin_52.fa -s 'Porphyromonas gingivalis' -r --no-self-update". Thanks for your patient reply

azat-badretdin commented 2 months ago

It looks like you are not requesting airgapped execution, so the nature of your, as determined now, persistent internet problem baffles me.

One of the IPs mentioned, 199.59.148.201, resolves to a Twitter host: r-199-59-148-201.twttr.com. The originating request also comes from a third party: docker.

So two third party host are failing while trying to talk to each other. This must be something that could be observed from our end, but we haven't seen it on 23rd of August, a day after you posted this problem, when we did our massive weekly test that involves installation of PGAP on multiple cloud computers.

I would recommend to consult local specialists that are familiar with your local internet setup.

Bottom line: we can't reproduce this Internet connection problem.

PS. I presume that when you reported that you retried, you also observed the same sort of error diagnostics, correct?