Hi ! Friends in the QIIME2 forum! I am very sorry to disturb you, but I encountered a problem with dada2 that I have no clues to solve.
The process is displayed following:
- USE FASTP TO PERFORM QUALITY CONTROL ON FIVE PAIRED-END SAMPLE
There were totally five paired-end samples used fastp to perform quality control and generated trimmed fastq files - IMPORT TRIMMED FASTQ FILES TO QIIME2
I imported the trimmed fastq files into QIIME2 through the following code:
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path manifeat_paired.tsv \
--output-path paired_debug.qza \
--input-format PairedEndFastqManifestPhred33V2
- CUTADAPT WAS USED TO CUT PRIMERS
To remove the primers, I preformedcutadaptplugin through the following code:
qiime cutadapt trim-paired \
--i-demultiplexed-sequences paired_debug.qza \
--p-front-f CCTACGGGAGGCAGCAG \
--p-front-r CCGTCAATTCMTTTRAGT \
--o-trimmed-sequences trim_debug_paired_end.qza
DADA2ERROR
Thedada2codes and error is presenting here:
qiime dada2 denoise-paired \
--i-demultiplexed-seqs trim_debug_paired_end.qza \
--p-trunc-len-f 0 \
--p-trunc-len-r 0 \
--p-n-threads 20 \
--o-table table_debug.qza \
--o-representative-sequences rep-seqs_debug.qza \
--o-denoising-stats denoising-stats_debug.qza
Plugin error from dada2:
Mismatching dimensions along axis 0: {0, 1}
Debug info has been saved to /tmp/qiime2-q2cli-err-kqv_zy8d.log
The /tmp/qiime2-q2cli-err-kqv_zy8d.log file is attached here:
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_dada.R --input_directory /tmp/tmpyop0vjwm/forward --input_directory_reverse /tmp/tmpyop0vjwm/reverse --output_path /tmp/tmpyop0vjwm/output.tsv.biom --output_track /tmp/tmpyop0vjwm/track.tsv --filtered_directory /tmp/tmpyop0vjwm/filt_f --filtered_directory_reverse /tmp/tmpyop0vjwm/filt_r --truncation_length 0 --truncation_length_reverse 0 --trim_left 0 --trim_left_reverse 0 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 20 --learn_min_reads 1000000
R version 4.3.3 (2024-02-29)
Loading required package: Rcpp
DADA2: 1.30.0 / Rcpp: 1.0.12 / RcppParallel: 5.1.6
2) Filtering .....
3) Learning Error Rates
11800 total bases in 43 reads from 5 samples will be used for learning the error rates.
11013 total bases in 43 reads from 5 samples will be used for learning the error rates.
3) Denoise samples .....
.....
5) Remove chimeras (method = consensus)
6) Report read numbers through the pipeline
7) Write output
Traceback (most recent call last):
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in __call__
results = self._execute_action(
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "<decorator-gen-49>", line 2, in denoise_paired
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self._callable_executor_(
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 367, in denoise_paired
return _denoise_helper(biom_fp, track_fp, hashed_feature_ids,
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 178, in _denoise_helper
table = table.concat(table_to_add)
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/biom/table.py", line 3609, in concat
concat_mat = stack([t.matrix_data for t in padded_tables])
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/scipy/sparse/_construct.py", line 733, in hstack
return _block([blocks], format, dtype, return_spmatrix=True)
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/scipy/sparse/_construct.py", line 908, in _block
blocks = [[_stack_along_minor_axis(blocks[b, :], 1)] for b in range(M)]
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/scipy/sparse/_construct.py", line 908, in <listcomp>
blocks = [[_stack_along_minor_axis(blocks[b, :], 1)] for b in range(M)]
File "/home/zcw/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/scipy/sparse/_construct.py", line 648, in _stack_along_minor_axis
raise ValueError(f'Mismatching dimensions along axis {other_axis}: '
ValueError: Mismatching dimensions along axis 0: {0, 1}
Then I checked .qzv file of paired_debug.qza by following code:
qiime demux summarize \
--i-data paired_debug.qza \
--o-visualization demux_debug_seqs.qzv
The demux_debug_seqs.qzv looks normally so that I can't tell where is the wrong. The demux_debug_seqs.qzv is attached to here.
demux_debug_seqs.qzv (319.7 KB)
Thank you very much for reading my post, and I truly appreciate any guidance you can provide.
