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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Problems with anvio-load-sqm (in the run-HMMs step) #761

Closed jahid10 closed 5 months ago

jahid10 commented 7 months ago

Hello,

I have recently tried to parse my SQM project (coassembled) into anvi'o databases with the anvi-load-sqm.py script. My project is run with Squeezemeta 1.5 and anvi'o version is 7.1

Here is the snippet of the problem: Screenshot_18

Here's the command I used to load my project: python3 /home/bioinfo/anaconda3/envs/SqueezeMeta/SqueezeMeta/utils/anvio_utils/anvi-load-sqm.py -p /media/bioinfo/hdd2/Metagenome_jute/metagenom_run_final --run-HMMS --min-contig-length 1200 -o /media/bioinfo/hdd2/Metagenome_jute/metagenom_run_final/anvio_result

fpusan commented 6 months ago

What's the output when you run directly the command written at the end of your message? anvi-run-hmms... etc

fpusan commented 6 months ago

Also what's the output of anvi-self-test?

fpusan commented 6 months ago

Can confirm this works for me with anvio v7 and the latest SqueezeMeta release. However the anvio7 conda package didn't work out of the box and I had to fiddle around with several package versions in order to get anvi-self-test working