Hello everyone,
I am trying to get results with DADA2 using the following command:
qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux-paired-end.qza
--p-trim-left-f 10
--p-trim-left-r 10
--p-trunc-len-f 0
--p-trunc-len-r 0
--p-trunc-q 25
--o-table 25_table.qza
--o-representative-sequences 25_rep-seqs.qza
--o-denoising-stats 25_denoising-stats.qza
I have also tried changed the values of trimming and truncation ,and I added > --p-n-threads 12 , and value of 20 too, but I am get the same error all the time:
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/qiime2-q2cli-err-h7kw6iqr.log
When I open the log I get:
Command: run_dada_paired.R /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/forward /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/reverse /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/output.tsv.biom /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/track.tsv /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r 232 232 10 10 2.0 2.0 25 consensus 1.0 1 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3
- Filtering The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/28_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/28_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/34_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/34_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/35_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/35_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/36_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/36_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/42_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/42_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/43_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/43_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/45_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/45_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/50_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/50_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/55_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/55_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/56_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/56_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/58_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/58_S1_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f/59_S1_L001_R1_001.fastq.gz and /var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r/59_S1_L001_R2_001.fastq.gz not written.
Some input samples had no reads pass the filter.
.x.....xxx.....xx.x....xxx.xx...... - Learning Error Rates
22200 total bases in 100 reads from 23 samples will be used for learning the error rates.
Error in err[c(1, 6, 11, 16), ] <- 1 :
número de subscritos incorretos en matriz
Ejecución interrumpida
Traceback (most recent call last):
File "/Users/alfonso/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 234, in denoise_paired
run_commands([cmd])
File "/Users/alfonso/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/alfonso/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/forward', '/var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/reverse', '/var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/output.tsv.biom', '/var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/track.tsv', '/var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_f', '/var/folders/t6/rcnzmjhd70g53z6wk2td9nph0000gn/T/tmp98qmmi36/filt_r', '232', '232', '10', '10', '2.0', '2.0', '25', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/alfonso/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in call
results = action(**arguments)
File "</Users/alfonso/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-459>", line 2, in denoise_paired
File "/Users/alfonso/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/Users/alfonso/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "/Users/alfonso/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 249, 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.
I though there might be issues with memory space, but I friend of mine tried the same in her computer and she gets the same error.
Does someone know what could be happening here?
Thank you so much in advance!