dada2 denoise issues : qiime2-2019.4/lib/R/etc/ldpaths missing

dada2 denoise issues : qiime2-2019.4/lib/R/etc/ldpaths missing

Hey guys,
I have problem when using ‘qiime2-2019.4’.


   qiime dada2 denoise-paired \
                    --i-demultiplexed-seqs 2_sequences/demux_no_primer_${libname}.qza \
                    --p-trim-left-f 0 \
                    --p-trim-left-r 0 \
                    --p-trunc-len-f $tlf_new \
                    --p-trunc-len-r $tlr_new \
                    --p-n-threads $ppn \
                    --p-n-reads-learn 1000000 \
                    --o-table 2_sequences/table_${libname}.qza \
                    --o-representative-sequences 2_sequences/rep_seqs_${libname}.qza \
                    --o-denoising-stats 2_sequences/denoising-stats_${libname}.qza \
                    --p-min-fold-parent-over-abundance 8


miniconda3/envs/qiime2-2019.4/lib/R/etc/ldpaths: No such file or directory
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/tmp5493sz2g/forward /tmp/tmp5493sz2g/reverse /tmp/tmp5493sz2g/output.tsv.biom /tmp/tmp5493sz2g/track.tsv /tmp/tmp5493sz2g/filt_f /tmp/tmp5493sz2g/filt_r 222 230 0 0 2.0 2 consensus 8.0 5 1000000

Traceback (most recent call last):
  File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/", line 231, in denoise_paired
  File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/", line 36, in run_commands, check=True)
  File "miniconda3/envs/qiime2-2019.4/lib/python3.6/", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp5493sz2g/forward', '/tmp/tmp5493sz2g/reverse', '/tmp/tmp5493sz2g/output.tsv.biom', '/tmp/tmp5493sz2g/track.tsv', '/tmp/tmp5493sz2g/filt_f', '/tmp/tmp5493sz2g/filt_r', '222', '230', '0', '0', '2.0', '2', 'consensus', '8.0', '5', '1000000']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/", line 311, in __call__
    results = action(**arguments)
  File "<miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/>", line 2, in denoise_paired
  File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/", line 231, in bound_callable
    output_types, provenance)
  File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/", line 365, in _callable_executor_
    output_views = self._callable(**view_args)
  File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/", line 246, 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.

Whenever I run the above command, the file(qiime2-2019.4/lib/R/etc/ldpaths) is always lost for no reason.

Welcome to the forum!
Looks like you don't have enough of RAM to run dada2. Did you try to allocate more RAM or decrease number of threads (it can decrease RAM requirement)?


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