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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 10 months ago

jahid10 commented 11 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 11 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 11 months ago

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

fpusan commented 11 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