Hello all! I am new to Qiime2, and after finally being able to import stuff into the virtual machine, I am having some problem doing quality control and pair end joining with my test data. I am running qiime2-2020.2 via Virtualbox, and below is my code (with verbose) and its associated error:
Code:
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trunc-len-f 230 --p-trunc-len-r 210 --p-trim-left-f 19 --p-trim-left-r 20 --p-n-threads 7 --o-representative-sequences dada2_rep_seq_16s.qza --o-table dada2_table_feature.qza --p-trunc-q 10 --p-max-ee-f 2.5 --o-denoising-stats dada2_denoise --verbose
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_paired.R /tmp/tmp6w2ny275/forward /tmp/tmp6w2ny275/reverse /tmp/tmp6w2ny275/output.tsv.biom /tmp/tmp6w2ny275/track.tsv /tmp/tmp6w2ny275/filt_f /tmp/tmp6w2ny275/filt_r 230 210 19 20 2.5 2.0 10 consensus 1.0 7 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.3 / RcppParallel: 4.4.4
- Filtering Error in names(answer) <- names1 :
'names' attribute [22] must be the same length as the vector [6]
Execution halted
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp6w2ny275/forward', '/tmp/tmp6w2ny275/reverse', '/tmp/tmp6w2ny275/output.tsv.biom', '/tmp/tmp6w2ny275/track.tsv', '/tmp/tmp6w2ny275/filt_f', '/tmp/tmp6w2ny275/filt_r', '230', '210', '19', '20', '2.5', '2.0', '10', 'consensus', '1.0', '7', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-455>", line 2, in denoise_paired
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2020.2/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.
What does this error mean? It seems like there is a mismatch between the length of my attribute and the length of my vector, but I'm not sure how to fix it. Thank you for all of your support!