Hello All. I update qiime2-2019.4 to qiime2-2019.7 and the picrust2 qiime plug-in using conda (in ubuntu desktop) following the tutorial. In qiime2-2019.4, picrust2 run smoothly without any error on my dataset (whole community). However, we are interested on the functions of the differentially abundant OTUS detected by Aldex in R. So I created a separate text file containing only the representative sequences of differentially abundant OTUS and the OTU abundance file, which I successfully converted to biom format and exported as qiime artifacts (.qza). The workflow run smoothly until I got an error in the qiime picrust2 custom-tree-pipeline. This is the same workflow that I used in the whole community dataset.
Based on this: Sequence ids don't overlap at metagenome pipeline step · Issue #16 · picrust/picrust2 · GitHub the error is likely caused by the differences the the sequences identifier in the repseq and OTU abundance file. I think that in my case representative sequences are not a problem because I used qiime2 dada2 plug-in and I have checked that sequence IDs in fasta and table are the same.
I attached here the files that I used and the workflow that I used. Any suggestions on how to proceed with this error will be greatky appreciatted.
Thank you very much.
(qiime2-2019.7) mmbl@mmbl:~/Desktop/picrust/spongeballs_Aldex2$ qiime picrust2 custom-tree-pipeline --i-table ballspongeOTUtableforpicrust_v2.qza --i-tree insert_ballsponge_picrust/tree.qza --output-dir spongeballs_Aldex2_picrust2 --p-threads 2 --p-hsp-method mp --p-max-nsti 2 --verbose
Running the below commands:
hsp.py -i 16S -t /tmp/tmpo7fbcumv/placed_seqs.tre -p 1 -n -o /tmp/tmpo7fbcumv/picrust2_out/16S_predicted.tsv.gz -m mp
hsp.py -i EC -t /tmp/tmpo7fbcumv/placed_seqs.tre -p 2 -o /tmp/tmpo7fbcumv/picrust2_out/EC_predicted.tsv.gz -m mp
hsp.py -i KO -t /tmp/tmpo7fbcumv/placed_seqs.tre -p 2 -o /tmp/tmpo7fbcumv/picrust2_out/KO_predicted.tsv.gz -m mp
metagenome_pipeline.py -i /tmp/tmpo7fbcumv/intable.biom -m /tmp/tmpo7fbcumv/picrust2_out/16S_predicted.tsv.gz -f /tmp/tmpo7fbcumv/picrust2_out/EC_predicted.tsv.gz -o /tmp/tmpo7fbcumv/picrust2_out/EC_metagenome_out --max_nsti 2.0
Error running this command:
metagenome_pipeline.py -i /tmp/tmpo7fbcumv/intable.biom -m /tmp/tmpo7fbcumv/picrust2_out/16S_predicted.tsv.gz -f /tmp/tmpo7fbcumv/picrust2_out/EC_predicted.tsv.gz -o /tmp/tmpo7fbcumv/picrust2_out/EC_metagenome_out --max_nsti 2.0
Standard output of failed command:
""
Standard error of failed command:
"0 of 46 ASVs were above the max NSTI cut-off of 2.0 and were removed.
Traceback (most recent call last):
File "/home/mmbl/miniconda3/envs/qiime2-2019.7/bin/metagenome_pipeline.py", line 122, in
main()
File "/home/mmbl/miniconda3/envs/qiime2-2019.7/bin/metagenome_pipeline.py", line 104, in main
skip_norm=args.skip_norm)
File "/home/mmbl/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/picrust2/metagenome_pipeline.py", line 68, in run_metagenome_pipeline
pred_marker)
File "/home/mmbl/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/picrust2/util.py", line 358, in three_df_index_overlap_sort
"input files.")
ValueError: No sequence ids overlap between all three of the input files.
"
ballspongeOTUtableforpicrust_v2.tsv (4.7 KB) ballspongeOTUtableforpicrust_v2.qza (10.4 KB) ballspongeforpicrust_v2.qza (9.3 KB)