Hi Thermokarst,
I got a similar error. I am trying qiime2 with a small set of 9 samples. The files are .bz2, I converted to .gz, renamed to cassava 1.8 standard format (I haven't change the set number ''_001" in any of them, I hope that is fine), examples of the conversion below:
NG-12583_4A03_lib191453_5405_1_1.fastq.gz -> L4A03_1_L001_R1_001.fastq.gz
NG-12583_4A03_lib191453_5405_1_2.fastq.gz -> L4A03_1_L001_R2_001.fastq.gz
NG-12583_4A04_lib191453_5405_1_1.fastq.gz -> L4A04_1_L001_R1_001.fastq.gz
NG-12583_4A04_lib191453_5405_1_2.fastq.gz -> L4A04_1_L001_R2_001.fastq.gz
NG-12583_4A05_lib191453_5405_1_1.fastq.gz -> L4A05_1_L001_R1_001.fastq.gz
NG-12583_4A05_lib191453_5405_1_2.fastq.gz -> L4A05_1_L001_R2_001.fastq.gz
(name of the samples: 4A03, 4A04, 4A05)
Then I imported the data with:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /mnt/fastqfiles/GATC-04/test
--source-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path demux-paired-end.qza
then:
qiime demux summarize \
--i-data demux-paired-end.qza \
--o-visualization demux-summary.qzv
and finally this, where I got the error:
qiime dada2 denoise-paired \
--p-trim-left-f 10 \
--p-trim-left-r 10 \
--p-trunc-len-f 260 \
--p-trunc-len-r 210 \
--p-max-ee 3 \
--p-trunc-q 2 \
--p-n-threads 0 \
--i-demultiplexed-seqs demux-paired-end.qza \
--o-representative-sequences rep-seqs.qza \
--o-table table.qza \
--verbose;
The error I got is:
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/tmp1nuehqcl/forward /tmp/tmp1nuehqcl/reverse /tmp/tmp1nuehqcl/output.tsv.biom /tmp/tmp1nuehqcl/filt_f /tmp/tmp1nuehqcl/filt_r 260 210 10 10 3.0 2 consensus 1.0 0 1000000
R version 3.3.2 (2016-10-31)
Loading required package: Rcpp
DADA2 R package version: 1.2.1
1) Filtering ...................
2) Learning Error Rates
2a) Forward Reads
Initial error matrix unspecified. Error rates will be initialized to the maximum possible estimate from this data.
Initializing error rates to maximum possible estimate.
Sample 1 - 922654 reads in 125731 unique sequences.
Sample 2 - 883708 reads in 116308 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
Convergence after 6 rounds.
2b) Reverse Reads
Initial error matrix unspecified. Error rates will be initialized to the maximum possible estimate from this data.
Initializing error rates to maximum possible estimate.
Sample 1 - 922654 reads in 156636 unique sequences.
Sample 2 - 883708 reads in 151915 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
selfConsist step 7
Convergence after 7 rounds.
3) Denoise remaining samples .................
The sequences being tabled vary in length.
4) Remove chimeras (method = consensus)
Error in isBimeraDenovo(unqs[[i]], ..., verbose = verbose) :
unused argument (method = "consensus")
Calls: removeBimeraDenovo -> isBimeraDenovo
Execution halted
Traceback (most recent call last):
File "/home/mothur/anaconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/home/mothur/anaconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/home/mothur/anaconda3/envs/qiime2-2017.10/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp1nuehqcl/forward', '/tmp/tmp1nuehqcl/reverse', '/tmp/tmp1nuehqcl/output.tsv.biom', '/t mp/tmp1nuehqcl/filt_f', '/tmp/tmp1nuehqcl/filt_r', '260', '210', '10', '10', '3.0', '2', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mothur/anaconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/commands.py", line 218, in __call__
results = action(**arguments)
File "<decorator-gen-338>", line 2, in denoise_paired
File "/home/mothur/anaconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", line 220, in bound_callable
output_types, provenance)
File "/home/mothur/anaconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", line 355, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/mothur/anaconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 194, 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."
I haven't remove the primers (10 bp), but I thought with the comand --p-trim-left-f 10
--p-trim-left-r 10 I am doing this already, please correct me if that is absolutely wrong. I am also using conda not miniconda, could be this also the problem? Many thanks in advance for your help! 
Ana.
