Hi everyone, I was trying to do picrust2 analysis for my data, I was using custom-tree-pipeline for my analysis. I had successfully constructed the SEPP tree.. Then followed as given in the PiCRUST2 tutorial.
qiime picrust2 custom-tree-pipeline --i-table Pyro-dada2-denoise/pyro-LogMPIE-table.qza --i-tree Downloads/Galaxy24-[picrust-tree.qza].qza --p-threads 8 --output-dir PiCRUST2-pyro-LOgMPIE-results --p-max-nsti 2 --p-highly-verbose --verbose
Running the below commands:
hsp.py -i 16S -t /tmp/tmpqtcoxpy6/placed_seqs.tre -p 1 -n -o /tmp/tmpqtcoxpy6/picrust2_out/16S_predicted.tsv.gz -m mp --verbose
Rscript /home/sreevatshan/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/Rscripts/castor_nsti.R /tmp/tmpqtcoxpy6/placed_seqs.tre /tmp/tmp5q4j9t3g/known_tips.txt /tmp/tmp5q4j9t3g/nsti_out.txt
Rscript /home/sreevatshan/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/Rscripts/castor_hsp.R /tmp/tmpqtcoxpy6/placed_seqs.tre /tmp/tmpgm21nsf1/subset_tab_0 mp FALSE FALSE /tmp/tmpfiluqyri/predicted_counts.txt /tmp/tmpfiluqyri/predicted_ci.txt 100
hsp.py -i EC -t /tmp/tmpqtcoxpy6/placed_seqs.tre -p 8 -n -o /tmp/tmpqtcoxpy6/picrust2_out/EC_predicted.tsv.gz -m mp --verbose
Error running this command:
hsp.py -i EC -t /tmp/tmpqtcoxpy6/placed_seqs.tre -p 8 -n -o /tmp/tmpqtcoxpy6/picrust2_out/EC_predicted.tsv.gz -m mp --verbose
Standard output of the above failed command:
Standard error of the above failed command:
Rscript /home/sreevatshan/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/Rscripts/castor_nsti.R /tmp/tmpqtcoxpy6/placed_seqs.tre /tmp/tmpoc1a9qer/known_tips.txt /tmp/tmpoc1a9qer/nsti_out.txt