benjjneb
issue with qiime dada2 denoise-ccs
Hi @benjjneb I have 24 clean CCS read datasets and i want to get amplicon sequence variants by running dada2. I got one issue when running dada2 denoise-ccs with QIIME2.
- First, when i am running dada2 in qiime2 with all 24 samples:
The command I used was:
qiime dada2 denoise-ccs --i-demultiplexed-seqs reads_qza/ccs_reads.qza --p-min-len 1200 --p-max-len 1800 --p-front AGRGTTYGATYMTGGCTCAG --p-adapter RGYTACCTTGTTACGACTT --p-n-threads 40 --o-table dada2_output/table.qza --o-representative-sequences dada2_output/representative_sequences.qza --o-denoising-stats dada2_output/stats.qza --verbose
The debug for this error is 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/qiime2/zcw/data/bc625311-79dd-4d22-b6e8-aefa5e8e080b/data --output_path /tmp/tmpuxwxzmu_/output.tsv.biom --output_track /tmp/tmpuxwxzmu_/track.tsv --removed_primer_directory /tmp/tmpuxwxzmu_/nop --filtered_directory /tmp/tmpuxwxzmu_/filt --forward_primer AGRGTTYGATYMTGGCTCAG --reverse_primer RGYTACCTTGTTACGACTT --max_mismatch 2 --indels False --truncation_length 0 --trim_left 0 --max_expected_errors 2.0 --truncation_quality_score 2 --min_length 1200 --max_length 1800 --pooling_method independent --chimera_method consensus --min_parental_fold 3.5 --allow_one_off False --num_threads 40 --learn_min_reads 1000000 --homopolymer_gap_penalty NULL --band_size 32
R version 4.1.3 (2022-03-10) Loading required package: Rcpp DADA2: 1.22.0 / Rcpp: 1.0.9 / RcppParallel: 5.1.5
- Removing Primers Read in 12234, output 0 (0%) filtered sequences. Read in 10596, output 0 (0%) filtered sequences. Error in sapply(match.fwd, end) + 1 : non-numeric argument to binary operator Execution halted Traceback (most recent call last): File "/home/kuma/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/denoise.py", line 410, in denoise_ccs run_commands([cmd]) File "/home/kuma/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/denoise.py", line 36, in run_commands subprocess.run(cmd, check=True) File "/home/kuma/miniconda3/envs/qiime2-2022.8/lib/python3.8/subprocess.py", line 516, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/qiime2/zcw/data/bc625311-79dd-4d22-b6e8-aefa5e8e080b/data', '--output_path', '/tmp/tmpuxwxzmu/output.tsv.biom', '--output_track', '/tmp/tmpuxwxzmu/track.tsv', '--removed_primer_directory', '/tmp/tmpuxwxzmu_/nop', '--filtered_directory', '/tmp/tmpuxwxzmu_/filt', '--forward_primer', 'AGRGTTYGATYMTGGCTCAG', '--reverse_primer', 'RGYTACCTTGTTACGACTT', '--max_mismatch', '2', '--indels', 'False', '--truncation_length', '0', '--trim_left', '0', '--max_expected_errors', '2.0', '--truncation_quality_score', '2', '--min_length', '1200', '--max_length', '1800', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '3.5', '--allow_one_off', 'False', '--num_threads', '40', '--learn_min_reads', '1000000', '--homopolymer_gap_penalty', 'NULL', '--band_size', '32']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/kuma/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.`
Is it possible caused by the input of the clean reads, since no primers have to be removed? Can you help me with this?
We don't support the Q2 plugin in this forum. You'll want to repost this on the QIIME2 forum: https://forum.qiime2.org/
