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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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anvi-setup-scg-taxonomy and anvi-setup-ncbi-cogs error #2172

Closed magueos closed 7 months ago

magueos commented 8 months ago

Short description of the problem

I am trying to run the command line "anvi-setup-scg-taxonomy" and "anvi-setup-ncbi-cogs" is sending me the same error everytime

anvi'o version

Anvi'o version is 7

System info

It was installed in the institute cluster by the admin and by using the container singularity

Detailed description of the issue

I am in an anvio container (singularity v 3.7.0) and I am trying to setup the databases, I tried by writting only the commands and also by seting up the path for each database: anvi-setup-scg-taxonomy anvi-setup-ncbi-cogs

I am having the following errors everytime: for anvi-setup-scg-taxonomy: Config Error: Something went wrong and DIAMOND did not create the database file it was supposed to for Ribosomal_S2 :(

for anvi-setup-ncbi-cogs:

COG version ..................................: COG20 COG data source ..............................: The anvi'o default. COG base directory ...........................: /opt/conda/envs/anvioenv/lib/python3.6/site-packages/anvio/data/misc/COG

Config Error: So the COG data directory is not there, and anvi'o wants to create one. But it didn't go that well. It could be due to permissions (which may require you to run this with sudo or may need to ask your sys admin to do it for you since this is a one time operation), or it could be due to something totally irrelevant. Here is the error message: [Errno 30] Read-only file system: '/opt/conda/envs/anvioenv/lib/python3.6/site-packages/anvio/data/misc/COG'.

Files / commands to reproduce the issue

A diamond-log-file.txt appeared in my directory:

DATE: 10 Nov 23 13:34:04

CMD LINE: diamond makedb --in /tmp/tmp_k1kxyd0/Ribosomal_S2 -d /opt/conda/envs/anvioenv/lib/python3.6/site-packages/anvio/data/misc/SCG_TAXONOMY/GTDB/SCG_SEARCH_DATABASES/Ribosomal_S2.dmnd -p 1

diamond v2.0.6.144 (C) Max Planck Society for the Advancement of Science Documentation, support and updates available at http://www.diamondsearch.org

CPU threads: 1

Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Database input file: /tmp/tmp_k1kxyd0/Ribosomal_S2 Opening the database file... Read-only file system [0s] Error: Error opening file /opt/conda/envs/anvioenv/lib/python3.6/site-packages/anvio/data/misc/SCG_TAXONOMY/GTDB/SCG_SEARCH_DATABASES/Ribosomal_S2.dmnd [10 Nov 23 13:34:04] diamond makedb cmd ...........................: diamond makedb --in /tmp/tmp_k1kxyd0/Ribosomal_S2 -d /opt/conda/envs/anvioenv/lib/python3.6/site-packages/anvio/data/misc/SCG_TAXONOMY/GTDB/SCG_SEARCH_DATABASES/Ribosomal_S2.dmnd -p 1 [10 Nov 23 13:34:04] Diamond search db ............................: /opt/conda/envs/anvioenv/lib/python3.6/site-packages/anvio/data/misc/SCG_TAXONOMY/GTDB/SCG_SEARCH_DATABASES/Ribosomal_S2.dmnd.dmnd

ivagljiva commented 8 months ago

Hi @magueos , please update to anvi'o version 8 by following these instructions and then try this command again. If the error persists, please let us know, and if that fixes the problem, then please close this issue. Thank you!

magueos commented 7 months ago

it worked, thank you very much !!