Not Outputting Correct Files

[ashdederich]

I downloaded the most recent version of eggnog-mapper available through conda and ran emapper.py with a .faa file as input.

I gave it the following options:

• use diamond blast
• ignore diamond warnings
• the --dmnd_algo option
• I said 'yes' to decorate_gff
• I gave it the --excel flag

When it finishes executing, I am missing all of the output files. There are no output files generated with the "prefix.emapper." beginning. What is going on?

Here is the command I ran for context:

emapper.py --cpu 16 -i 17978X1_NODE_1_length_607754_cov_33.762272.fasta.faa.gz -o eggnog17978X1 -output_dir $SCRDIR --override -m diamond --dmnd_ignore_warnings --dmnd_algo ctg --decorate_gff yes --excel

Here, $SCRDIR is an environment variable I created that leads to my scratch directory.

[Cantalapiedra]

Hi @ashdederich ,

I am not sure what could be happening. Did you try running it in a local directory? Did emapper.py finished OK? What are the contents of the $SCRDIR after the emapper.py run?

Let's see if we can figure it out.

Best, Carlos

[ashdederich]

Hi @Cantalapiedra,

I feel silly. I just reran it on a local directory to test it out to give you more information, and it turns out I was missing one of the dashes in the --output_dir (I ran it as -output_dir). I was originally running this in the scratch dir on my local HPC, and it wasn't throwing an error to my slurm output files.

After fixing this error, it is returning all correct files (I received 5 with the output prefix, ending in .annotations, .annotations.xlsx, .gff, .hits, and .seed_orthologs).

Thank you for taking the time to look into this!

Best Ashley

[Cantalapiedra]

Hi @ashdederich ,

jaja I didn't notice the missing "-" in your previous message. You are right. Glad that it worked at last!

Best, Carlos

[Cantalapiedra]

Hi,

I will close this issue. Please, re-open or re-issue if needed.

Best, Carlos