Error running pipcrust2_pipeline.py

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Dimitrios-Marinos Karadedos

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Feb 18, 2025, 8:28:30 AMFeb 18

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Hello there,

I execute:

picrust2_pipeline.py -s results_ncbi_16S_all_barcodes/otu_99_cleaned.fa -i results_ncbi_16S_all_barcodes/cluster/99/otu_cluster_99.tsv -o picrust2_out_3 --processes 8 --verbose

it runs for 4 to 6 hours and then returns this error:

Error running this command:
epa-ng --tree /mnt/ssd2/KaradedosDM/new_picrust2/picrust2-2.4.1/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa picrust2_out_all_barcodes/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query picrust2_out_all_barcodes/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 1 -m /mnt/ssd2/KaradedosDM/new_picrust2/picrust2-2.4.1/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w picrust2_out_all_barcodes/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100

The version of picrust2 that I am using is the latest (v2.6.0)

Robyn Wright

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Feb 18, 2025, 8:44:05 AMFeb 18

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Hi there,

Could you please attach (as a text file, ideally) the full output that you get? And can you also give some details of the computer that you're using for running PICRUSt2 (OS, how much RAM, etc), please?