Hey guys,
I have ran these commands before facing error on dada2:
Activated qiime2 through conda:
conda activate qiime2-2020.8
Ran fastqc:
fastqc -t 12 -o SRR068049.fastq.gz
Imported fastq to qza:
qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /work/microbiomapsi/liviacmg/bbMGYS0278/data --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path /work/microbiomapsi/liviacmg/bbMGYS0278/SRR068049.qza
Ran cutadapt (it is single-end):
Before run cutadapt, verified if there were the forward and reverse primers informed on the article:
grep -c "AGAGTTTGATCCTGGCTCAG" SRR068049.fastq
grep -c "TGCTGCCTCCCGTAGGAGT" SRR068049.fastq
(there were only the last one, this is why i cutted it)
qiime cutadapt trim-single --i-demultiplexed-sequences SRR068049.qza --p-cores 6 --p-front TGCTGCCTCCCGTAGGAGT --p-discard-untrimmed --p-minimum-length 200 --output-dir trim.cutadapt
Error trying to run dada2:
qiime dada2 denoise-single --i-demultiplexed-seqs trimmed_sequences.qza --p-trim-left 0 --p-trunc-len 230 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza --p-n-threads 4 --verbose
The output was this 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_single.R /tmp/qiime2-archive-fnz3e6nu/8eabe224-00fb-4cca-8815-118b6ccdf44a/data /tmp/tmpqglsz62j/output.tsv.biom /tmp/tmpqglsz62j/track.tsv /tmp/tmpqglsz62j 230 0 2.0 2 Inf independent consensus 1.0 4 1000000 NULL 16
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.4.6 / RcppParallel: 5.0.0
- Filtering .
- Learning Error Rates
16560 total bases in 72 reads from 1 samples will be used for learning the error rates.
Error in err[c(1, 6, 11, 16), ] <- 1 :
incorrect number of subscripts on matrix
Execution halted
Traceback (most recent call last):
File "/usr/local/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 181, in _denoise_single
run_commands([cmd])
File "/usr/local/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/usr/local/miniconda3/envs/qiime2-2020.8/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/tmp/qiime2-archive-fnz3e6nu/8eabe224-00fb-4cca-8815-118b6ccdf44a/data', '/tmp/tmpqglsz62j/output.tsv.biom', '/tmp/tmpqglsz62j/track.tsv', '/tmp/tmpqglsz62j', '230', '0', '2.0', '2', 'Inf', 'independent', 'consensus', '1.0', '4', '1000000', 'NULL', '16']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_single
File "/usr/local/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/usr/local/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/usr/local/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 218, in denoise_single
band_size='16')
File "/usr/local/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 192, in _denoise_single
" 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.
I discarded the option of memory problem because i tried to run on PBS on server and also tried to run on a newer version of qiime2. I also saw somewhere that it could be the R version, for the person it worked on R version 3.3, but i don't know if it is the problem or how to do this, because I think the R is automatically installed within conda.
Help!!
