Hi Guys,
I am getting a following error.
qiime dada2 denoise-paired --i-demultiplexed-seqs Combined.qza --p-trim-left-f 0 --p-trunc-len-f 260 --p-trim-left-r 0 --p-trunc-len-r 260 --o-representative-sequences trimmed-dada2.qza --o-table trimmed_table-dada2.qza --o-denoising-stats trimmed_stats-dada2.qza --verbose
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/tmpnnfv5q4c/forward /tmp/tmpnnfv5q4c/reverse /tmp/tmpnnfv5q4c/output.tsv.biom /tmp/tmpnnfv5q4c/track.tsv /tmp/tmpnnfv5q4c/filt_f /tmp/tmpnnfv5q4c/filt_r 260 260 0 0 2.0 2 consensus 1.0 1 1000000
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
-
Filtering …
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Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 13 reads in 9 unique sequences.
Sample 2 - 13 reads in 10 unique sequences.
selfConsist step 2
Convergence after 2 rounds.
2b) Reverse Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 13 reads in 13 unique sequences.
Sample 2 - 13 reads in 13 unique sequences.
selfConsist step 2
Convergence after 2 rounds. -
Denoise remaining samples
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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/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
run_commands([cmd])
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpnnfv5q4c/forward’, ‘/tmp/tmpnnfv5q4c/reverse’, ‘/tmp/tmpnnfv5q4c/output.tsv.biom’, ‘/tmp/tmpnnfv5q4c/track.tsv’, ‘/tmp/tmpnnfv5q4c/filt_f’, ‘/tmp/tmpnnfv5q4c/filt_r’, ‘260’, ‘260’, ‘0’, ‘0’, ‘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/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-442>”, line 2, in denoise_paired
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/home/alakshmanan/bin/miniconda3/envs/qiime2-2019.1/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.
Help me to fix this issue.
Thanks in advance.
By
Arun