Kegg output errors

55 views
Skip to first unread message

Frederick Shi

unread,
Aug 20, 2021, 11:26:23 AM8/20/21
to picrust-users
Hi,
I am running the pipeline and for some reason, the "metagenome_pipeline.py" for KO_metagenome is giving weird errors. I ran it before and it worked fine for the whole pipeline. It also worked with EC and pathway for this dataset. 


When running the full pipeline, I got an error:
Error running this command:
metagenome_pipeline.py --input asv_rare.biom --function ../picrust2_output/KO_predicted.tsv.gz --marker ../picrust2_output/marker_predicted_and_nsti.tsv.gz --min_reads 1 --min_samples 1 --out_dir ../picrust2_output/KO_metagenome_out --metagenome_contrib --max_nsti 2.0 --strat_out

Standard output of failed command:
""

Standard error of failed command:
""

and when I ran "metagenome_pipeline.py" it gives "Killed: 9" 

I wonder if anyone can help.

Thanks,

Gavin Douglas

unread,
Aug 20, 2021, 3:44:07 PM8/20/21
to picrus...@googlegroups.com
Hey there,

That likely means that you have insufficient RAM unfortunately as that can be an obstacle sometimes when processing the KO data as it is larger than the EC number or pathway data outputs. How much RAM do you have?

One quick fix could be to update to the latest version of PICRUSt2 though - what version are you currently running?


Cheers,

Gavin

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/6ed73e3a-15f7-4c50-beec-9203c1d2bc44n%40googlegroups.com.

Message has been deleted

Frederick Shi

unread,
Aug 22, 2021, 7:46:14 PM8/22/21
to picrust-users
Hi Gavin,
I was using an old version of PICRUSt2. I updated it to the lastest version and it worked.

Thanks!
Reply all
Reply to author
Forward
0 new messages