Error while running DADA2 in R (return code 1)

Hi Qiimers,

Getting the following error when using DADA2 step:

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 /tmp/qiime2-q2cli-err-rzuw81bp.log

Command I was running was as follows:

qiime dada2 denoise-paired --i-demultiplexed-seqs 1_demux-paired-end.qza --p-trim-left-f 0 --p-trunc-len-f 278 --p-trim-left-r 7 --p-trunc-len-r 223 --o-representative-sequences 2_rep-seqs.qza --o-table 2_table.qza --p-n-threads 6

and the debug info:

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/tmp5r9aae0r/forward /tmp/tmp5r9aae0r/reverse /tmp/tmp5r9aae0r/output.tsv.biom /tmp/tmp5r9aae0r/filt_f /tmp/tmp5r9aae0r/filt_r 278 223 0 7 2.0 2 consensus 1.0 6 1000000

R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
1) Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF,  :
  These are the errors (up to 5) encountered in individual cores...
Error in writeFastq(fqF, fout[[1]], "w", compress = compress) :
  failed to write record 23726
Error in writeFastq(fqR, fout[[2]], "a", compress = compress) :
  failed to write record 10058
Error in writeFastq(fqR, fout[[2]], "w", compress = compress) :
  failed to write record 52285
Error in writeFastq(fqR, fout[[2]], "w", compress = compress) :
  failed to write record 2275
Error in writeFastq(fqF, fout[[1]], "w", compress = compress) :
  failed to write record 196
Execution halted
Traceback (most recent call last):
  File "/home/denir/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
    run_commands([cmd])
  File "/home/denir/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
    subprocess.run(cmd, check=True)
  File "/home/denir/anaconda3/envs/qiime2-2018.2/lib/python3.5/subprocess.py", line 398, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp5r9aae0r/forward', '/tmp/tmp5r9aae0r/reverse', '/tmp/tmp5r9aae0r/output.tsv.biom', '/tmp/tmp5r9aae0r/filt_f', '/tmp/tmp5r9aae0r/filt_r', '278', '223', '0', '7', '2.0', '2', 'consensus', '1.0', '6', '1000000']' returned non-zero exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/denir/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 246, in __call__
    results = action(**arguments)
  File "<decorator-gen-354>", line 2, in denoise_paired
  File "/home/denir/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
    output_types, provenance)
  File "/home/denir/anaconda3/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/denir/anaconda3/envs/qiime2-2018.2/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.

The samples were imported as demultiplexed paired using manifest file (with already removed barcodes by sequencing centre):

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path filenames.txt --output-path 1_demux-paired-end.qza --source-format PairedEndFastqManifestPhred33

I am aware similar errors have been addressed before, but I am not really able to pinpoint what is going on here.
Any help is appreciated :slight_smile:

Deni

1 Like

Just an update

It seems there was a problem with /tmp directory, either writing permissions or memory issue.

After defining new tmp path to my ~/.bashrc, for which I am sure I have writing permission and sufficient storage the analysis seems to be running fine for now.

I’ll keep you updated.

Best,
Deni

4 Likes

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