Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-246fgnfr.log
The following is in my log file-
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/tmp0lee7zg3/forward /tmp/tmp0lee7zg3/reverse /tmp/tmp0lee7zg3/output.tsv.biom /tmp/tmp0lee7zg3/filt_f /tmp/tmp0lee7zg3/filt_r 150 150 13 13 2.0 2 consensus 1.0 1 1000000
R version 3.3.2 (2016-10-31)
Loading required package: Rcpp
There were 50 or more warnings (use warnings() to see the first 50)
DADA2 R package version: 1.4.0
1) Filtering ....
2) Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 47247 reads in 7216 unique sequences.
Sample 2 - 64347 reads in 8628 unique sequences.
Sample 3 - 5292 reads in 1591 unique sequences.
Sample 4 - 48223 reads in 5545 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
Convergence after 6 rounds.
2b) Reverse Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 47247 reads in 23249 unique sequences.
Sample 2 - 64347 reads in 28165 unique sequences.
Sample 3 - 5292 reads in 3718 unique sequences.
Sample 4 - 48223 reads in 21266 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
Convergence after 4 rounds.
3) Denoise remaining samples
4) Remove chimeras (method = consensus)
Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) :
Input must be a valid sequence table.
Calls: removeBimeraDenovo -> isBimeraDenovoTable
In addition: Warning message:
In is.na(colnames(unqs[[i]])) :
is.na() applied to non-(list or vector) of type 'NULL'
Execution halted
Traceback (most recent call last):
File "/home/mim/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/home/mim/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/home/mim/miniconda3/envs/qiime2-2017.10/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp0lee7zg3/forward', '/tmp/tmp0lee7zg3/reverse', '/tmp/tmp0lee7zg3/output.tsv.biom', '/tmp/tmp0lee7zg3/filt_f', '/tmp/tmp0lee7zg3/filt_r', '150', '150', '13', '13', '2.0', '2', '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 "/home/mim/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/commands.py", line 218, in __call__
results = action(**arguments)
File "<decorator-gen-338>", line 2, in denoise_paired
File "/home/mim/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", line 220, in bound_callable
output_types, provenance)
File "/home/mim/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py", line 355, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/mim/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 194, 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.
Summary
Summary
Kindly guide me.