having an issue running this bit of code :
qiime dada2 denoise-ccs
--i-demultiplexed-seqs single-end-demux.qza
--p-front AGRGTTYGATYMTGGCTCAG
--p-adapter RGYTACCTTGTTACGACTT
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats stats.qza
And getting the error:
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/wzs/data/0878bf38-672c-47a0-b99c-59104fa196cb/data --output_path /tmp/tmpzmr33lcc/output.tsv.biom --output_track /tmp/tmpzmr33lcc/track.tsv --removed_primer_directory /tmp/tmpzmr33lcc/nop --filtered_directory /tmp/tmpzmr33lcc/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 20 --max_length Inf --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
Warning message:
package ‘optparse’ was built under R version 4.2.3
R version 4.2.2 (2022-10-31)
Loading required package: Rcpp
DADA2: 1.26.0 / Rcpp: 1.0.11 / RcppParallel: 5.1.6
- Removing Primers
Multiple matches to the primer(s) in some sequences. Using the longest possible match.
37435 sequences out of 70098 are being reverse-complemented.
Read in 70098, output 65145 (92.9%) filtered sequences.
37805 sequences out of 71571 are being reverse-complemented.
Read in 71571, output 66352 (92.7%) filtered sequences.
42466 sequences out of 78060 are being reverse-complemented.
Read in 78060, output 73357 (94%) filtered sequences.
51210 sequences out of 95513 are being reverse-complemented.
Read in 95513, output 89794 (94%) filtered sequences.
41621 sequences out of 78047 are being reverse-complemented.
Read in 78047, output 72317 (92.7%) filtered sequences.
46968 sequences out of 88577 are being reverse-complemented.
Read in 88577, output 82087 (92.7%) filtered sequences.
53831 sequences out of 100071 are being reverse-complemented.
Read in 100071, output 93249 (93.2%) filtered sequences.
50287 sequences out of 92889 are being reverse-complemented.
Read in 92889, output 87638 (94.3%) filtered sequences.
38152 sequences out of 70070 are being reverse-complemented.
Read in 70070, output 66029 (94.2%) filtered sequences.
38919 sequences out of 72084 are being reverse-complemented.
Read in 72084, output 67199 (93.2%) filtered sequences.
40407 sequences out of 77521 are being reverse-complemented.
Read in 77521, output 70579 (91%) filtered sequences.
40102 sequences out of 73974 are being reverse-complemented.
Read in 73974, output 69222 (93.6%) filtered sequences.
16483 sequences out of 34522 are being reverse-complemented.
Read in 34522, output 31644 (91.7%) filtered sequences.
49248 sequences out of 93451 are being reverse-complemented.
Read in 93451, output 85795 (91.8%) filtered sequences.
45902 sequences out of 86363 are being reverse-complemented.
Read in 86363, output 80497 (93.2%) filtered sequences.
50229 sequences out of 91686 are being reverse-complemented.
Read in 91686, output 86687 (94.5%) filtered sequences.
39402 sequences out of 74164 are being reverse-complemented.
Read in 74164, output 68148 (91.9%) filtered sequences.
47761 sequences out of 88493 are being reverse-complemented.
Read in 88493, output 83236 (94.1%) filtered sequences.
47384 sequences out of 87274 are being reverse-complemented.
Read in 87274, output 81938 (93.9%) filtered sequences.
58730 sequences out of 109833 are being reverse-complemented.
Read in 109833, output 102091 (93%) filtered sequences.
49969 sequences out of 91399 are being reverse-complemented.
Read in 91399, output 86485 (94.6%) filtered sequences.
37813 sequences out of 71108 are being reverse-complemented.
Read in 71108, output 66602 (93.7%) filtered sequences.
46261 sequences out of 88987 are being reverse-complemented.
Read in 88987, output 80898 (90.9%) filtered sequences.
53932 sequences out of 99876 are being reverse-complemented.
Read in 99876, output 93689 (93.8%) filtered sequences.
58512 sequences out of 108973 are being reverse-complemented.
Read in 108973, output 101820 (93.4%) filtered sequences.
35371 sequences out of 66654 are being reverse-complemented.
Read in 66654, output 62038 (93.1%) filtered sequences.
18085 sequences out of 34162 are being reverse-complemented.
Read in 34162, output 31407 (91.9%) filtered sequences.
........................... - Filtering ...........................
- Learning Error Rates
Traceback (most recent call last):
File "/home/wzs/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 440, in denoise_ccs
run_commands([cmd])
File "/home/wzs/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/wzs/anaconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/qiime2/wzs/data/0878bf38-672c-47a0-b99c-59104fa196cb/data', '--output_path', '/tmp/tmpzmr33lcc/output.tsv.biom', '--output_track', '/tmp/tmpzmr33lcc/track.tsv', '--removed_primer_directory', '/tmp/tmpzmr33lcc/nop', '--filtered_directory', '/tmp/tmpzmr33lcc/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', '20', '--max_length', 'Inf', '--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']' died with <Signals.SIGKILL: 9>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wzs/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in call
results = self._execute_action(
File "/home/wzs/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 539, in _execute_action
results = action(**arguments)
File "", line 2, in denoise_ccs
File "/home/wzs/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/wzs/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "/home/wzs/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 449, in denoise_ccs
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
I was not encountering this problem before.This came suddenly. It would be great if anyone could guide me.