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AvilPage / kraken-db-builder

Build standard & custom kraken2 database indexes with single command
https://avilpage.com/kdb.html
MIT License
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subprocess.CalledProcessError: #2

Open diegomd90 opened 1 week ago

diegomd90 commented 1 week ago

Hello Avil;

I'm having some issues while running:

kdb --db-type standard --threads 24 --cache-dir --no-check-certificate

And I got

`Traceback (most recent call last): File "/usr/lib/python3.10/concurrent/futures/process.py", line 246, in _process_worker r = call_item.fn(*call_item.args, **call_item.kwargs) File "/home/bioinformatica/.local/lib/python3.10/site-packages/kdb.py", line 71, in download_taxanomy subprocess.run(cmd, shell=True, check=True) File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'echo https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz | xargs -n 1 -P 4 wget -c' returned non-zero exit status 123. """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/bioinformatica/.local/bin/kdb", line 8, in sys.exit(main()) File "/home/bioinformatica/.local/lib/python3.10/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/home/bioinformatica/.local/lib/python3.10/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/home/bioinformatica/.local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/bioinformatica/.local/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/home/bioinformatica/.local/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, **kwargs) File "/home/bioinformatica/.local/lib/python3.10/site-packages/kdb.py", line 147, in main future1.result() File "/usr/lib/python3.10/concurrent/futures/_base.py", line 458, in result return self.get_result() File "/usr/lib/python3.10/concurrent/futures/_base.py", line 403, in get_result raise self._exception subprocess.CalledProcessError: Command 'echo https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz | xargs -n 1 -P 4 wget -c' returned non-zero exit status 123.`

ChillarAnand commented 5 days ago

@diegomd90 Did you run this command in your machine and check?

echo ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz | xargs -n 1 -P 4 wget -c

I am not seeing any issues with this step on this machine.