DADA2 return code -1 --> need specific help please!

Hi all,

My lab mate and I are trying to run the DADA2 step using qiime2-2019.7 through the super computer (MARCC) that we have access to through our institution. Our job failed and gave us return code 1. What do we need to change about our code to get it to successfully run? We do have the option to increase memory and # of cores, but we don't think that is the issue here.

See below text for the contents of the output from the verbose command:

(base) [[email protected]@bc-login02 ~]$ cat slurm-37205833.out
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3

  1. Filtering Error in writeFastq(fqF, fout[[1]], "a", compress = compress) :
    failed to write record 55732
    Execution halted
    Traceback (most recent call last):
    File "/home-1/[email protected]/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/denoise.py", line 234, in denoise_paired
    run_commands([cmd])
    File "/home-1/[email protected]/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 "/home-1/[email protected]/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', '/home-1/[email protected]/scratch/tmpcx5fbjm
    /forward', '/home-1/[email protected]/scratch/tmpcx5fbjm
    /reverse', '/home-1/[email protected]/scratch/tmpcx5fbjm_/output.tsv.biom', '/home-1/[email protected]/scratch/tmpcx5fbjm_/track.tsv', '/home-1/[email protected]/scratch/tmpcx5fbjm_/filt_f', '/home-1/[email protected]/scratch/tmpcx5fbjm_/filt_r', '93', '93', '3', '0', '2.0', '2.0', '2', 'consensus', '1.0', '1', '10000']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home-1/[email protected]/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in call
results = action(**arguments)
File "</home-1/[email protected]/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-459>", line 2, in denoise_paired
File "/home-1/[email protected]/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home-1/[email protected]/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 "/home-1/[email protected]/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.

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.
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 /home-1/[email protected]/scratch/tmpcx5fbjm_/forward /home-1/[email protected]/scratch/tmpcx5fbjm_/reverse /home-1/[email protected]/scratch/tmpcx5fbjm_/output.tsv.biom /home-1/[email protected]/scratch/tmpcx5fbjm_/track.tsv /home-1/[email protected]/scratch/tmpcx5fbjm_/filt_f /home-1/[email protected]/scratch/tmpcx5fbjm_/filt_r 93 93 3 0 2.0 2.0 2 consensus 1.0 1 10000


Here is the sequence quality plot that we based our trimming amounts off of:

And here is the code that we input for our job in MARCC:

#!/bin/bash
#SBATCH -p lrgmem
#SBATCH -c 10
#SBATCH -t 72:00:00
#SBATCH --mail-type=all
#SBATCH [email protected]
#SBATCH --job-name=DADA2-30-barcode-illumina-lrgmem

set -e
export TMPDIR=$HOME/scratch

qiime dada2 denoise-paired
--i-demultiplexed-seqs ~/work/Illumina_Data/paired-end-demux.qza
--p-trim-left-f 3
--p-trim-left-r 0
--p-trunc-len-f 93
--p-trunc-len-r 93
--p-n-reads-learn 10000
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza
--verbose


A post was merged into an existing topic: How many nodes can QIIME2 use?