R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4
- Filtering The filter removed all reads: /var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/filt_f/428_138_L001_R1_001.fastq.gz and /var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/filt_r/428_139_L001_R2_001.fastq.gz not written.
The filter removed all reads: /var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/filt_f/296-2_96_L001_R1_001.fastq.gz and /var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/filt_r/296-2_97_L001_R2_001.fastq.gz not written.
Some input samples had no reads pass the filter.
.........................................................................................................................................x....................x................................................................................................. - Learning Error Rates
289560551 total bases in 1067489 reads from 4 samples will be used for learning the error rates.
244454981 total bases in 1067489 reads from 4 samples will be used for learning the error rates. - Denoise remaining samples ..................................................................................................................................................................................................................................................Error in dada(drpR, err = errR, multithread = multithread, verbose = FALSE) :
Invalid derep$quals matrix. Quality values must be positive integers.
Execution halted
Traceback (most recent call last):
File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/forward', '/var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/reverse', '/var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/output.tsv.biom', '/var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/track.tsv', '/var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/filt_f', '/var/folders/yp/gmbd6_256wnbb6qyf3s3v_6r0000gn/T/tmpkg09sibn/filt_r', '0', '229', '0', '0', '2.0', '2.0', '2', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-459>", line 2, in denoise_paired
File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "/Users/karasnow/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 272, 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.