Comments (7)
Hmm.. Could you maybe post the full error message? Is it possible that no genes were called?
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so what it looks like here is that diamond just doesnt map anything to the reference db.. (this merged.genecalls.faa is a temporary file that you wouldnt get to see) Are there genes in the gene calls file? ill try make the error message more clear for the next version..
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So to test whether it was my genomes being too novel relative to the database, I ran gunc using an E. coli MG1655 genome. I'm still getting the same error message that it can't find the merged.genecalls.faa. file. The prodigal output is perfectly fine it just can't find the merged.genecalls.faa file.
Interestingly, I ran it again and specified the tmp directory. Got a different output error (see below) but the merged.genecalls.faa file was created this time.
Finally I specified an out directory just to see if it would help. But same error as above.
I'm not sure what's happening. gunc 1.0.4 is running in its own conda environment and so should be isolated from anything interfering with it.
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that is weird.. so i ran that same ecoli genome and it ran fine for me.. could you be having a problem with your storage..?
what happens if you run with --temp_dir /dev/shm
?
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I'm not sure whats happening.... I did a complete reinstall, including the database, and still same problem is happening. I tried giving it the protein calls from prodigal and still getting an error. The only thing I can think of is there some python module I'm missing on our server that's running CentOS? Other than that I've hit a brick wall!
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ok so after more investigation: the reason you got a different behaviour when you specified a temp_dir above (--tmp_dir gunc_temp
) was that the directory gunc_temp
didnt exist.. I will make sure to add a check for that in the next version..
So at least we have ruled that part out and we are back to why diamond fails.. How much effort do you want to go to here..?
If you wanted to, you could replace your /home/sheikc/cssheik/anaconda3/envs/GUNC/lib/python3.9/site-packages/gunc/external_tools.py
file with https://gist.github.com/fullama/d22863fcea9bbd1c66a691f8df990f5e
this will output a more detailed error message about why diamond failed..
..I will add better debugging output to the list of things for the next release..
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Related Issues (20)
- installation failure using conda HOT 5
- **conda install** no longer finds **diamond=2.0.4** HOT 9
- Diamond parameters - max-target-seqs HOT 4
- file_suffix flag HOT 24
- panda KeyError: 'contig' HOT 5
- false positives HOT 8
- NAN in the output result HOT 13
- apply GUNC to a large dataset of MAGs HOT 1
- Failed to run Diamond HOT 4
- Incompatibility with pandas 2.0 HOT 2
- diamond error HOT 4
- Command 'diamond --version' returned non-zero exit status 132 HOT 3
- --use_species_level is not a better choice? HOT 1
- --use_species_level is not a better choice? HOT 5
- Suppress deprecation warning from pandas HOT 1
- Threshold CSS values when dealing with genomes in reference database HOT 4
- New GTDB database release HOT 1
- GUNC gene_counts.json file not found! HOT 5
- GUNC diamond output filename HOT 1
- Database update for gunc
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