Kegg output errors

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Frederick Shi

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Aug 20, 2021, 11:26:23 AM8/20/21
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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

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Aug 20, 2021, 3:44:07 PM8/20/21
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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

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Frederick Shi

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

Thanks!
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