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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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anvi-load-sqm.py: At least one gene call in your external genes file ('5660473') contains a start position smaller than 0 #594

Closed jahid10 closed 1 year ago

jahid10 commented 1 year ago

Hi, I have run the anvi-load-sqm.py with the following command python3 /home/bioinfo/mambaforge/envs/SqueezeMeta/SqueezeMeta/utils/anvio_utils/anvi-load-sqm.py -p /media/bioinfo/Hilsa/Jahid_NGS_metagenomics/rrw_analysis -o /media/bioinfo/Hilsa/Jahid_NGS_metagenomics/rrw_analysis/anvio --num-threads 12 --min-contig-length 2500 --run-scg-taxonomy --run-HMMS

I found the following error.: File/Path Error: At least one gene call in your external genes file ('5660473') contains a start position smaller than 0. Anvi'o could extend your contigs with imaginary
nucleotides to make things work. Admittedly it would have been much more fun to do that instead of asking you to go back and correct your external gene calls
file. But we are burdened to act as adults here :(

Please let me know where should I modify the file

ggnatalia commented 1 year ago

Hi, sorry about the delay (I really did not have time until now to look at it). Could you tell me which version of SQM and anvio are you using? I'm pretty sure to have seen this problem before so I have an idea of what could be happening.

jahid10 commented 1 year ago

Hello ggnatalia, It was a long time ago. My SqueezeMeta version is 1.5.1 and my Anvio version is 7.1. I have successfully used anvio-load-sqm in other projects later without any problems.

ggnatalia commented 1 year ago

Ok, thanks! I'll try to reproduce it. Just in case (because it is related with your particular data), could you send me the _anvio_genes file which is within the sqm2anvio folder to look into (or send me the line from the 5660473 gene entry in this file)? I'm afraid it has a negative value coming from upstream results.

This should be created within the results folder.

jahid10 commented 1 year ago

Hello ggnatalia, Thanks for looking into the problem. I have attached the zipped the anvio_genes file here. If there anything else you need, please let me know. https://doc-0k-0k-docs.googleusercontent.com/docs/securesc/19nk8ghi0dk3vutba56ptqmdm2uk8e0q/65mptsc1gp5gu694nu2lsnoa2b0ma678/1678268025000/12020632922898716723/10845181473800859913/1YX0lxWzOjzMzqdTXjSb8JPQ3OzAweOpo?e=download&authuser=0

ggnatalia commented 1 year ago

Hi, I'm afraid I cannot open the link. Could you send the document to ngarcia@cnb.csic.es?