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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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problem with SqueezeMeta_conf.pl in anvio #734

Closed Azimdine closed 9 months ago

Azimdine commented 9 months ago

Dear all, After running SqueezeMeta with a big project, i would analyse my data using anvio interface (i have installed version 8). after running the script: python3 /pasteur/appa/homes/ahabib/miniconda3/envs/SqueezeMeta/SqueezeMeta/utils/anvio_utils/anvi-load-sqm.py -p Result -o /pasteur/zeus/projets/p02/Biomics/Bioinfo/projet_Ariane/Result/results/anvio --num-threads 12 --min-contig-length 2500 --run-scg-taxonomy --run-HMMS

i get this There must be some problem with "/pasteur/appa/homes/ahabib/miniconda3/envs/SqueezeMeta/SqueezeMeta/utils/anvio_utils/sqm2anvio.pl Result Result/results/sqm2anvio 8.0". It's better to stop and check it

and when i check the anvio-load-sm.logfile, i have this: Can't find SqueezeMeta_conf.pl in Result I don't understand because SqueezeMeta_conf.pl is in Result directory

Any suggestions, solutions? cordially Azim anvi-load-sqm.logfile.zip

jtamames commented 9 months ago

Hello Azim I understand that Result is the name of your project. Are you running the command in the upper directory? (I guess that must be projet_Ariane) Best, J

Azimdine commented 9 months ago

When i had lunch SqueezeMeta, -p was Result. script was SqueezeMeta.pl -m coassembly -p Result -s SN_B6781_1.txt -f B6781_1 --nopfam -b 20 -t 36

datas (fastq, SN_B6781_1.txt ...) was in projet_Ariane directory. So i thought that -p in anvio was to be Result.

I try with projet_Ariane as -p cordially Azim

Azimdine commented 9 months ago

i have the same result Can't find SqueezeMeta_conf.pl in projet_Ariane. Is the project path ok? at /pasteur/appa/homes/ahabib/miniconda3/envs/SqueezeMeta/SqueezeMeta/utils/anvio_utils/sqm2anvio.pl line 21.

jtamames commented 9 months ago

Yes, Result is the project, that's clear, but where are you running the anvi-load-sqm.py? You must run it in projet_Ariane directory

Azimdine commented 9 months ago

that's working thank you very much

jtamames commented 9 months ago

Great! Remember, yopu must run the script where you ran SqueezeMeta originally, OR, you can specify the full path for the project. That is, -p /pasteur/zeus/projets/p02/Biomics/Bioinfo/projet_Ariane/Result must work every time Best, J

Azimdine commented 9 months ago

thanks