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some conflicts and still can not run #1
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Thank you, dear Marie, for your help and update. I tried the slurm version, and unfortunately, it has some conflict yet. For example, in This is the summary of running:
What's your suggestion. How can we handle it and import these data to the SQL and go to the next step? |
Hi Naser, Sorry for my late reply, I have been trying to reproduce your issue but without success. I will try to update the Sincerely yours, |
Thank you very much for redeveloping this code. Yes, as you mentioned. NCBI has changed the structure of the database and some files. Recently for another tool, I needed This is the way I used to extract these files from existing NCBI accession2taxid files (may need to be added to the For extract gi_taxid_nucl.dmp.gz from acc2taxid.nucl (or from other accession2taxid files from https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/):
and for extract gi_taxid_prot.dmp.gz from acc2taxid.prot (or from other accession2taxid files from https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/):
Sincerely yours, Naser |
Link to issue from @poursalavati
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