Stopping at "Calculating Similarity Networks"

[Fiona Newberry]

Running vContact2 and it has stalled at “Calculating Similarity Networks”. I tried rerunning with the intermediate files as suggested but still stalling. The program doesn’t stop, it just stalls. Here’s the stdout:

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INFO:vcontact2: Found Diamond: /users/miniconda3/envs/vContact2/bin/diamond 
INFO:vcontact2: Found MCL: /users/miniconda3/envs/vContact2/bin/mcxload 
INFO:vcontact2: Identified 20 CPUs 
INFO:vcontact2: Using reference database: None 
WARNING:vcontact2: No reference database selected! vConTACT2 will be unable to run taxonomy-based performance metrics unless taxonomic information is included in the --proteins-fp file. 
INFO:vcontact2: Using existing directory vContact/output. 
INFO:vcontact2: Identified legacy (v1) vConTACT files. Reference databases will be ignored. Taxonomy will be ignored unless included in legacy files. 
INFO:vcontact2: Read 1498755 entries (dropped 7947 singletons) from vContact/output/vConTACT_profiles.csv  
============================This is vConTACT2 0.9.22============================    
----------------------------------Pre-Analysis----------------------------------   
------------------------------Reference databases-------------------------------   
----------------------------------Loading data----------------------------------   
------------------------Calculating Similarity Networks-------------------------

Thanks

[shailesh nair]

@Fiona Newberry Hi did you solve the problem? I am running into the same issue (5500 contigs processing on 50 threads )and it's been 72 hours showing “Calculating Similarity Networks”.

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[Fiona Newberry]

Hi,

The only work around I could find for this was to kill the command and restart it.

Sorry if that doesn't help much.

Kind Regards, Fiona

[shailesh nair]

Thank you for the quick reply. I did try that earlier. Probably, I will try killing all instances of dependencies and restarting.

Thank you.