[BUG] <title> HTTP Error 403: rate limit exceeded - Githubissues

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline

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[BUG] <title> HTTP Error 403: rate limit exceeded #213

Closed Gahyeon-K closed 2 years ago

Gahyeon-K commented 2 years ago

I tried to run PGAP, but error message: 'HTTP Error 403: rate limit exceeded' popped up. Is there any way to solve it? Thank you.

azat-badretdin commented 2 years ago

Thank you for your report!

Could you please post the logs? Screen capture, etc Thanks!

Gahyeon-K commented 2 years ago

There are no log files...:( Only 'HTTP Error 403: rate limit exceeded' lines appeared, and I can't find any log files sorry.

azat-badretdin commented 2 years ago

Let me clarify: you type your command line: ./pgap.py .... and all you get on screen is this?

Could you please post output ls -latr . in the directory you are running this?

Gahyeon-K commented 2 years ago

My command line: sudo ./pgap.py -n -o Input.yam Output ls -latr .: bedtools2 Anaconda3-2020.11-Linux-x86_64.sh pyani-0.2.11 miniconda.sh bedtools-2.29.1.tar.gz pilon-1.23.jar SPAdes-3.15.4-Linux.tar.gz . .profile examples.desktop .bash_logout .conda miniconda .bashrc quast gfapy assembly_graph.gfa NIBR_79 AGB agb_output NIBR_87 Porechop .test.vimrc.swp test.vimrc Flye index.html llvmorg-13.0.1 index.html.1 .ncftp development miniconda.html barrnap .ssh 37_Streptomyces .cpan .basespace Illumina cmake-3.23.2.tar.gz racon cmake-3.23.2 ALE Unicycler SPAdes-3.15.4-Linux .viminfo .config .cache 220705_pyani.txt 220705_ANIm_test .condarc v0.2.11.tar.gz BiG-SCAPE-master.zip Pfam-A.hmm Pfam-A.hmm.h3p Pfam-A.hmm.h3m Pfam-A.hmm.h3f Pfam-A.hmm.h3i .wget-hsts anaconda3 bin pgap.py .pgap .bash_history .Xauthority

azat-badretdin commented 2 years ago

Hmm.. Something is off with your command line: ./pgap.py -n -o Input.yam

-o parameter requires output directory following it, but it seems that Input.yam follows it. Not sure how this would work...

azat-badretdin commented 2 years ago

I also do not see Input.yam in the listing you posted... Thanks for posting it, BTW!

Gahyeon-K commented 2 years ago

When I ran before, this command did well! But, maybe after upgrade pgap it goes into trouble. I ran this command in the directory where 'Input.yam' is located. And when I use that command, outputs were saved at home.

azat-badretdin commented 2 years ago

this command did well!

That's what evil wants us to think when we do wrong :-)

I suspect that this sort of invocation leads to unpredictable results.

Could you please try to run it as specified in Quick Start notes https://github.com/ncbi/pgap/wiki/Quick-Start

./pgap.py -n -o some_output_dir your_input.yaml_file

?

Thanks!