diamond looking for wrong faa file

[SheikGeomicro]

Hi,

I just downloaded gunc using a conda install (v 1.0.4) and and diamond keeps failing because it is looking for "merged.genecalls.faa" and prodigal has created called genes file "input_genome_bin.faa". my command I've tried is: gunc run -i input_genome_bin.fa -r path/to/database/gunc_db_progenomes2.1.dmnd -t 2.

Seems like this is hard coded in and not something we can specify? But I might be missing something.

Thanks in advance.

[fullama]

Hmm.. Could you maybe post the full error message? Is it possible that no genes were called?

[SheikGeomicro]

So here is what I'm seeing in the terminal prompt. <img width="1025" alt="Screen Shot 2021-07-31 at 7 48 09 AM" src="https://user-images.githubusercontent.com/16261473/127853966-7039a530-1d41-4fa5-aa99-d3468887a338.png"> And here is what is showing up in the gene_calls output <img width="653" alt="Screen Shot 2021-07-31 at 7 49 23 AM" src="https://user-images.githubusercontent.com/16261473/127854134-60472e6f-404c-4595-880d-fd0992143fcc.png"> gunc seems to be looking for a merged.genecalls.faa and not the actual file output file from prodigal.

…

-C

On Sat, Jul 31, 2021 at 4:00 AM Anthony Fullam ***@***.***> wrote: Hmm.. Could you maybe post the full error message? Is it possible that no genes were called? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD4CCYIL5YYR2F4D2LZKKALT2O3RFANCNFSM5BJGVQHA> .

-- Cody Sheik Ph.D. Assistant Professor Department of Biology Large Lakes Observatory University of Minnesota Duluth 2205 East 5th Street Duluth, MN 55812 Ph. 1-218-726-8128 Twitter: @microbesheik

[fullama]

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..

[SheikGeomicro]

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.

[fullama]

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 ?

[SheikGeomicro]

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!

[fullama]

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..