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grp-bork / gunc

Python package for detection of chimerism and contamination in prokaryotic genomes.
GNU General Public License v3.0
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Failed to run Diamond #31

Closed ahmedmagds closed 1 year ago

ahmedmagds commented 1 year ago

I keep getting this error "Failed to run Diamond gunc_out/gene_calls/merged.genecalls.faa" gunc run -r gunc_db_progenomes2.1.dmnd -i genome4.fna -o gunc_out -e .fna When I check the gene_calls folder, I find genome4.genecalls.faa. Is this the issue that the program cannot find merged.....?

fullama commented 1 year ago

unfortunately the error message is not so informative (this will be fixed in the next version) would you like to send me the input file and i can look to see why diamond fails?

ahmedmagds commented 1 year ago

genome4.fna.txt.zip Sure, thanks for help!

ahmedmagds commented 1 year ago

@fullama It does seem installation issue. I tried to install it on our cluster and I also get this error. gunc -h Traceback (most recent call last): File "/home/ahmed/miniconda3/envs/gunc/bin/gunc", line 6, in <module> from gunc.gunc import main File "/home/ahmed/miniconda3/envs/gunc/lib/python3.6/site-packages/gunc/gunc.py", line 14, in <module> from . import visualisation as vis File "/home/ahmed/miniconda3/envs/gunc/lib/python3.6/site-packages/gunc/visualisation.py", line 4, in <module> import plotly.graph_objects File "/home/ahmed/miniconda3/envs/gunc/lib/python3.6/site-packages/plotly/__init__.py", line 35, in <module> from plotly import ( File "/home/ahmed/miniconda3/envs/gunc/lib/python3.6/site-packages/plotly/io/__init__.py", line 12, in <module> from ._renderers import renderers, show File "/home/ahmed/miniconda3/envs/gunc/lib/python3.6/site-packages/plotly/io/_renderers.py", line 7, in <module> from packaging.version import Version ModuleNotFoundError: No module named 'packaging' I also got this error when I tried to install it on my Mac M1. I solved this issue by updating python. I am not sure though is this caused problems downstream for diamond. I installed gunc using mamba create -n gunc -c bioconda gunc. . For some reason it installed gun 1.0.3 so I needed to update it using mamba update gunc. Let me know your thoughts and I appreciate your help.

fullama commented 1 year ago

ok so i have tried to run it multiple times and i cannot replicate the error.. did you get any other output? could diamond have run out of memory maybe?