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Code, unit tests, and tutorials for running PICRUSt2
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Issue with using picrust2 pipeline for ITS sequences #322

Closed dixi06 closed 8 months ago

dixi06 commented 1 year ago

I am new to pricrust2. I used the following code for fungi ITS sequences and get this error. Please let me know what is wrong?

picrust2_pipeline.py -s rep-seq4.fasta -i asv_its2_picrust.txt -o picrustout_Its2 -p 1 -r /home/AAFC-AAC/modid/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/fungi/fungi_ITS Warning - non-default reference files specified with default pathway mapfile of prokaryote-specific MetaCyc pathways (--pathway_map option). This usage may be unintended. Warning - 5586 input sequences aligned poorly to reference sequences (--min_align option specified a minimum proportion of 0.8 aligning to reference sequences). These input sequences will not be placed and will be excluded from downstream steps.

Error running this command: hsp.py --tree picrustout_Its2/out.tre --output picrustout_Its2/marker_predicted_and_nsti.tsv.gz --observed_trait_table /home/AAFC-AAC/modid/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/16S.txt.gz --hsp_method mp --edge_exponent 0.5 --seed 100 --calculate_NSTI --processes 1

Standard error of the above failed command:

Error running this command: Rscript /home/AAFC-AAC/modid/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/Rscripts/castor_hsp.R picrustout_Its2/out.tre /scratch/tmpskpeal0m/subset_tab_0 mp 0.5 FALSE FALSE /scratch/tmpe0vi_9bb/predicted_counts.txt /scratch/tmpe0vi_9bb/predicted_ci.txt 100

Standard error of the above failed command: Error: None of the reference ids within the function abundance table are found within the input tree. This can occur when malformed or mismatched custom reference files are used. Execution halted

gavinmdouglas commented 1 year ago

Hi there,

You can see that at the hsp.py step that you're pointing to the 16S-linked function table. Make sure that you change the appropriate parameters, as described here: https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions#how-can-i-run-a-custom-or-non-default-database-such-as-the-fungi-18s-and-its-databases

Please also note the warning in that FAQ answer about the ITS predictions!

Cheers,

Gavin

R-Wright-1 commented 8 months ago

I am just closing this issue as there hasn't been any follow-up for a while. Please let me know if this needs to be reopened.