Thank you Greg.
It ran almost 24 h. But no luck.
However, I could do it through Powershell (ubuntu) on Windows.
Secondly, I am processing Nanopore seq (full length 16S-1530 bp) with q score of 27 (average). It is failing at DADA2 (denoising step). Any ideas would be great to resolve it.
(qiime2-2023.2) jvrao001@BCC-A92859:~$ qiime dada2 denoise-ccs --i-demultiplexed-seqs reads_qza/rawSeq.qza --p-min-len 1200 --p-max-len 1500 --p-front GCATCAGRRTTYGATYHTGGYTYAG --p-adapter GCATCRGYTACCTTGTTAYGACTT --o-table dada2_output/table.qza --o-representative-sequences dada2_output/representative_sequences.qza --o-denoising-stats dada2_output/stats.qza --verbose
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/jvrao001/data/9e39f766-f9f1-4ba0-b153-e6321c5ff58f/data --output_path /tmp/tmpb7pkmji8/output.tsv.biom --output_track /tmp/tmpb7pkmji8/track.tsv --removed_primer_directory /tmp/tmpb7pkmji8/nop --filtered_directory /tmp/tmpb7pkmji8/filt --forward_primer GCATCAGRRTTYGATYHTGGYTYAG --reverse_primer GCATCRGYTACCTTGTTAYGACTT --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 1500 --pooling_method independent --chimera_method consensus --min_parental_fold 3.5 --allow_one_off False --num_threads 1 --learn_min_reads 1000000 --homopolymer_gap_penalty NULL --band_size 32
R version 4.2.2 (2022-10-31)
Loading required package: Rcpp
DADA2: 1.26.0 / Rcpp: 1.0.10 / RcppParallel: 5.1.6
- Removing Primers
Multiple matches to the primer(s) in some sequences. Using the longest possible match.
9763 sequences out of 24842 are being reverse-complemented.
Read in 24842, output 15080 (60.7%) filtered sequences.
11440 sequences out of 30184 are being reverse-complemented.
Read in 30184, output 18684 (61.9%) filtered sequences.
11863 sequences out of 29921 are being reverse-complemented.
Read in 29921, output 19308 (64.5%) filtered sequences.
7763 sequences out of 21784 are being reverse-complemented.
Read in 21784, output 12471 (57.2%) filtered sequences.
11106 sequences out of 28244 are being reverse-complemented.
Read in 28244, output 17582 (62.3%) filtered sequences.
14352 sequences out of 35740 are being reverse-complemented.
Read in 35740, output 22722 (63.6%) filtered sequences.
8965 sequences out of 23520 are being reverse-complemented.
Read in 23520, output 14370 (61.1%) filtered sequences.
11119 sequences out of 29175 are being reverse-complemented.
Read in 29175, output 17806 (61%) filtered sequences.
8845 sequences out of 23824 are being reverse-complemented.
Read in 23824, output 14375 (60.3%) filtered sequences.
7465 sequences out of 20226 are being reverse-complemented.
Read in 20226, output 12340 (61%) filtered sequences.
6194 sequences out of 17519 are being reverse-complemented.
Read in 17519, output 9937 (56.7%) filtered sequences.
11922 sequences out of 29422 are being reverse-complemented.
Read in 29422, output 19417 (66%) filtered sequences.
11115 sequences out of 28489 are being reverse-complemented.
Read in 28489, output 17486 (61.4%) filtered sequences.
13090 sequences out of 32819 are being reverse-complemented.
Read in 32819, output 20881 (63.6%) filtered sequences.
10105 sequences out of 26629 are being reverse-complemented.
Read in 26629, output 16127 (60.6%) filtered sequences.
14275 sequences out of 34658 are being reverse-complemented.
Read in 34658, output 23565 (68%) filtered sequences.
9087 sequences out of 23609 are being reverse-complemented.
Read in 23609, output 14270 (60.4%) filtered sequences.
10518 sequences out of 26983 are being reverse-complemented.
Read in 26983, output 17086 (63.3%) filtered sequences.
8339 sequences out of 22789 are being reverse-complemented.
Read in 22789, output 13355 (58.6%) filtered sequences.
6231 sequences out of 16397 are being reverse-complemented.
Read in 16397, output 10042 (61.2%) filtered sequences.
5912 sequences out of 16829 are being reverse-complemented.
Read in 16829, output 9639 (57.3%) filtered sequences.
4402 sequences out of 12716 are being reverse-complemented.
Read in 12716, output 7219 (56.8%) filtered sequences.
12786 sequences out of 31226 are being reverse-complemented.
Read in 31226, output 20184 (64.6%) filtered sequences.
7242 sequences out of 19459 are being reverse-complemented.
Read in 19459, output 11908 (61.2%) filtered sequences.
17643 sequences out of 44509 are being reverse-complemented.
Read in 44509, output 29346 (65.9%) filtered sequences.
......................... - Filtering The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_UroA1_17_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_UroA2_18_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_UroA3_19_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_UroA4_20_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_UroA5_21_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_UroA6_22_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_UroA7_23_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_UroA8_24_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_VEH1_9_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_VEH2_10_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_VEH3_11_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_VEH4_12_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_VEH5_13_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_VEH6_14_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_VEH7_15_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/As_VEH8_16_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/UroA1_4_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/UroA2_5_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/UroA3_6_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/UroA4_7_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/UroA5_8_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/VEH1_0_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/VEH2_1_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/VEH3_2_L001_R1_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpb7pkmji8/filt/VEH4_3_L001_R1_001.fastq.gz not written.
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Error: No reads passed the filter (was truncLen longer than the read length?)
Traceback (most recent call last):
File "/home/jvrao001/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 440, in denoise_ccs
run_commands([cmd])
File "/home/jvrao001/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/jvrao001/miniconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/qiime2/jvrao001/data/9e39f766-f9f1-4ba0-b153-e6321c5ff58f/data', '--output_path', '/tmp/tmpb7pkmji8/output.tsv.biom', '--output_track', '/tmp/tmpb7pkmji8/track.tsv', '--removed_primer_directory', '/tmp/tmpb7pkmji8/nop', '--filtered_directory', '/tmp/tmpb7pkmji8/filt', '--forward_primer', 'GCATCAGRRTTYGATYHTGGYTYAG', '--reverse_primer', 'GCATCRGYTACCTTGTTAYGACTT', '--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', '1500', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '3.5', '--allow_one_off', 'False', '--num_threads', '1', '--learn_min_reads', '1000000', '--homopolymer_gap_penalty', 'NULL', '--band_size', '32']' returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jvrao001/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in denoise_ccs
File "/home/jvrao001/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/jvrao001/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/jvrao001/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 443, in denoise_ccs
raise ValueError(
ValueError: No reads passed the filter. trunc_len (0) may be longer than read lengths, or other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.
Plugin error from dada2:
No reads passed the filter. trunc_len (0) may be longer than read lengths, or other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.
See above for debug info.
Thanks Greg.