search

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
357 stars 78 forks source link

anvi-load-sqm.py : process stops midway and does not create the PROFILES.db #620

Closed Sneha-bioinfo closed 4 months ago

Sneha-bioinfo commented 1 year ago

Hi, I have been trying to run anvi-load-sqm.py on my SqueezeMeta outputs (sequential mode outputs). While the script runs correctly , it stops after sometime and is unable to create the PROFILE.db and throws an error. When I check the sqm2anvio results directory, I can see that the bam files have been correcty created and the CONTIGS.db has also been created in the results, but the tool fails to create PROFILES.db. The diamond version I have installed in my conda environment is 0.9.14 as suggested. I wonder if its a memory issue? The error -

Config Error: Bad news. The database search operation failed somewhere :( It is very hard for anvi'o to know what happened, but this is what we heard last: 'list index out of range'. If this error message makes sense ot you, great. Otherwise a LIKELY reason for this failure is that you have a diamond version installed on your system that is incompatible with anvi'o :/ The best course of action for that is to make sure running diamond --version on your terminal returns 0.9.14. If not, try to upgrade/downgrade your diamond to match this version. If you are in a conda environmnet you can try running conda install diamond=0.9.14. Please feel free to contact us if the problem persists. We apologize for the inconvenience.

ggnatalia commented 1 year ago

Hi, Sorry about the delay, I did not have time to look at it before. Could you tell me which version of SQM and anvi'o are you using, so that I can reproduce the problem?

Sneha-bioinfo commented 1 year ago

Hi! The versions used were as follows- SQM- v1.6.0- one gg for many baskets SqueezeMeta- 1.6.0 Anvi= v7.1 (hope)

ggnatalia commented 1 year ago

Ok, thank you! I'll try to reproduce it.

fpusan commented 8 months ago

Sorry we've missed this. If still interested, I think the best would be that you share your project with us and I will try to reproduce it. I've been recently testing anvio7 (bioconda version) together with the latest SqueezeMeta version, and it works with my test dataset.

fpusan commented 4 months ago

Closing due to lack of activity, feel free to reopen