Hello All
I successfully installed qiimepicrust2 after trying so many time, but the whole credit goes to the QIIME team where the members guided me step by step for successful installation.
Thanks.
Now while running the command I faced an unexpected error
“stopping - no asv ids overlap between input fasta and sequence abundance table” at the first time however when I ran at the second time It gave and new error
Simply “Killed”
Please suggest
Thanks a lot @ andrewsanchez
I tried couple of times and got the things done.
Thank you for this support
However while running the command
qiime picrust2 full-pipeline --i-table Narwani_final/Narwanitable.qza --i-seq Narwani_final/Narwani_clustered_sequences.97.qza --output-dir Narwani_q2-picrust2_output --p-threads 1 --p-hsp-method pic --p-max-nsti 2 --verbose
Stopping - no ASV ids overlap between input FASTA and sequence abundance table
Please suggest
Hello Again
I opted for the alternative way of the analysis by
Swapping in SEPP for read placement with q2 picrust2 and ran the first command I got an error
place_seqs.py -s Narwani_final/Narwani_clustered_sequences/dna-sequences.fasta -o out.tre -p 1 --intermediate intermediate/place_seqs/epa_out/epa_result.jplace
Warning - 41 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.
This is the set of poorly aligned input sequences to be excluded: 836908, 4297918, 109469, 2456449, 250705, 521852, 328281, 208800, 3407058, 4406763, 237889, 779617, 323600, 4348417, 182490, 4469859, 706095, 2432071, 74159, 583766, 131662, 242389, 4396376, 1110769, 737413, 714536, 193866, 774802, 4386673, 4421746, 1124836, 91492, 211578, 4383626, 4446022, 548510, 1119783, 651305, 259220, 712007, 357092
Error running this command:
epa-ng --tree /home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa intermediate/place_seqs/epa_out/epa_result.jplace/ref_seqs_hmmalign.fasta --query intermediate/place_seqs/epa_out/epa_result.jplace/study_seqs_hmmalign.fasta --chunk-size 5000 -T 1 -m /home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w intermediate/place_seqs/epa_out/epa_result.jplace/epa_out --filter-acc-lwr 0.99 --filter-max 100
Standard output of the above failed command:
INFO Selected: Output dir: intermediate/place_seqs/epa_out/epa_result.jplace/epa_out/
INFO Selected: Query file: intermediate/place_seqs/epa_out/epa_result.jplace/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre
INFO Selected: Reference MSA: intermediate/place_seqs/epa_out/epa_result.jplace/ref_seqs_hmmalign.fasta
INFO Selected: Filtering by accumulated threshold: 0.99
INFO Selected: Maximum number of placements per query: 100
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model
INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.453141 (user), weights&rates: (0.25,0.0250674) (0.25,0.220229) (0.25,0.782933) (0.25,2.97177)
Base frequencies (user): 0.229585 0.22008 0.298596 0.251739
Substitution rates (user): 1.00319 2.79077 1.5301 0.87441 3.83966 1
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 1
INFO ______ ____ ___ _ __ ______
/ // __ \ / | / | / // /
/ __/ / // // /| | ______ / |/ // / __
/ / / // ___ |/_____// /| // // /
/_____/// // || // |/ __/ (v0.3.6)
Please suggest
Hello thank you all
I tracked the error in both commands the first one is beause of difference in header ids in biom table and sequences
And the second one is memmory issue.
Bur now my point is how to solve the ist case, I mean to match the ids in biom file similar to that of seq.
If any command please mention.
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