Working through the atacama soils tutorial I’ve encountered an error when including “–p-n-threads 0”. The same error has occured for any thread value over 22 in my testing (machine has 56 threads available).
The problem seems to center on the vector length not matching the number of names. The size of the vector varies from 72 to 74.
Here is the copy-pasted command and the results using the --verbose argument
In this example the threads used is 24, but this is consistent with the error for any large thread value.
qiime dada2 denoise-paired --verbose
–i-demultiplexed-seqs demux.qza
–p-trim-left-f 13
–p-trim-left-r 13
–p-trunc-len-f 150
–p-trunc-len-r 150
–p-n-threads 24
–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats denoising-stats.qza
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_paired.R /tmp/tmpg_zeokr9/forward /tmp/tmpg_zeokr9/reverse /tmp/tmpg_zeokr9/output.tsv.biom /tmp/tmpg_zeokr9/track.tsv /tmp/tmpg_zeokr9/filt_f /tmp/tmpg_zeokr9/filt_r 150 150 13 13 2.0 2.0 2 consensus 1.0 24 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.1 / Rcpp: 1.0.3 / RcppParallel: 4.4.4
- Filtering The filter removed all reads: /tmp/tmpg_zeokr9/filt_f/YUN2029.3_65_L001_R1_001.fastq.gz and /tmp/tmpg_zeokr9/filt_r/YUN2029.3_65_L001_R2_001.fastq.gz not written.
Error in sendMaster(try(lapply(X = S, FUN = FUN, …), silent = TRUE)) : **
** write error, closing pipe to the master
Error in names(answer) <- names1 : **
** ‘names’ attribute [75] must be the same length as the vector [72]
Execution halted
Traceback (most recent call last):
File “/home/abletha689957dl/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 257, in denoise_paired
run_commands([cmd])
File “/home/abletha689957dl/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/abletha689957dl/anaconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpg_zeokr9/forward’, ‘/tmp/tmpg_zeokr9/reverse’, ‘/tmp/tmpg_zeokr9/output.tsv.biom’, ‘/tmp/tmpg_zeokr9/track.tsv’, ‘/tmp/tmpg_zeokr9/filt_f’, ‘/tmp/tmpg_zeokr9/filt_r’, ‘150’, ‘150’, ‘13’, ‘13’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘24’, ‘1000000’]’ returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/abletha689957dl/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</home/abletha689957dl/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-459>”, line 2, in denoise_paired
File “/home/abletha689957dl/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/abletha689957dl/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/abletha689957dl/anaconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 272, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
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.