dada2 denoise issues : qiime2-2019.4/lib/R/etc/ldpaths missing
Hey guys,
I have problem when using ‘qiime2-2019.4’.
Command:
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
error:
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/_denoise.py", line 231, in denoise_paired
run_commands([cmd])
File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "miniconda3/envs/qiime2-2019.4/lib/python3.6/subprocess.py", 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/commands.py", line 311, in __call__
results = action(**arguments)
File "<miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-451>", line 2, in denoise_paired
File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable_executor_
output_views = self._callable(**view_args)
File "miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", 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.