Thanks for the reply. I ran the script with the different truncating points and verbose flab and this is the error. any input is appreciated.
qiime dada2 denoise-paired
--i-demultiplexed-seqs paired-end-demux.qza
--p-trim-left-f 30
--p-trim-left-r 23
--p-trunc-len-f 278
--p-trunc-len-r 266
--o-representative-sequences oral_rep-seqs-DADA2_v1.qza
--o-table oral_table_v1.qza
--o-denoising-stats oral_DADA2-stats_v1.qza
--verbose
(qiime2-2020.6) [tmad3197@login1 FASTQ_raw_saliva_V1]$ cat job01.e7421204
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/R/library/RCurl/libs/RCurl.so':
/lib64/libc.so.6: version `GLIBC_2.14' not found (required by /usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/R/library/RCurl/libs/../../../.././libssl.so.1.1)
Execution halted
Traceback (most recent call last):
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 264, in denoise_paired
run_commands([cmd])
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/pbs.7421204.pbsserver/tmp5px6l6fv/forward', '/tmp/pbs.7421204.pbsserver/tmp5px6l6fv/reverse', '/tmp/pbs.7421204.pbsserver/tmp5px6l6fv/output.tsv.biom', '/tmp/pbs.7421204.pbsserver/tmp5px6l6fv/track.tsv', '/tmp/pbs.7421204.pbsserver/tmp5px6l6fv/filt_f', '/tmp/pbs.7421204.pbsserver/tmp5px6l6fv/filt_r', '278', '266', '30', '23', '2.0', '2.0', '2', 'independent', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 279, 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.
