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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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enrichm annotate KO frequency table but all zeros #121

Open mhyleung opened 3 years ago

mhyleung commented 3 years ago

Dear all

I ran the following command:

ENRICHM_DB=/directory_to/enrichm_database

enrichm annotate --output /current directory/output_annotate_ko --ko_hmm --genome_directory /current_directory/input_bin_genome --threads 24 --log /current_directory/log --force --verbosity 5

When the run has finished (which ran without error), the /current directory/output_annotate_ko/ I have the following outputs:

annotations_genomes (directory) annotations_gff (directory) annotations_ko_hmm (directory) genome_genes (directory) genome_proteins (directory) ko_hmm_frequency_table.tsv (file)

When I tried to open the above file, I do see the KOs row names and the sample row names, but everything is zero, in that there's absolutely no coding sequences from my input genome bins that were assigned as a KO.

Alternatively, I used prodigal outputs from the one of the genomes to run KofamKOALA, and it returned 1,277 KO entry matches. I am pretty sure there are some KOs in my data.

Just as another note, when I ran the same command as above, but instead of --ko_hmm I ran --ko, actually the ko_frequency table.tsv file is nowhere to be found.

I have enrichm version 0.6.3

Thanks

Marc

geronimp commented 3 years ago

Hi again Marc,

Thanks for the error report. You're correct there should be KO annotations being produced, but I am also unable to reproduce this error using the current version of enrichm. Are you able to provide a small, reproducible example of the error so that I can investigate the issue further

mhyleung commented 3 years ago

Dear geronimp

Thanks for the response. There actually is no error message. The run appears to have run fine. Just that the output files do not seem complete.

I notice that the latest version on github is 0.5.0, but I got the conda installation which is v0.6.3. Could that be in any way related to the issue I am encountering?

May I DM you my log file if that is ok? Thanks for your help!

Regards

Marcus

biohuzi commented 2 years ago

Hi, I had the same problem as yours when using enrichm (KO frequency table were all zeros), have you solved this problem?