Hi
I have imported some paired-end reads(generated by a simulator) to qiime (version qiime2-2019.1). The simulator produced one fastq file (interleaved) for each sample. To import I have used extract_reads_from_interleaved_file.py. Then Imported to qiime using following command
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path fastq_manifest
–output-path paired-end-demux.qza
–input-format PairedEndFastqManifestPhred33
After visualize the demux.qzv
I want to use following command to denoise
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --output-dir dada2/ --o-representative-sequences rep-seqs --p-trim-left-f 20 --p-trim-left-r 20 --p-trunc-len-f 150 --p-trunc-len-r 140 --p-n-threads 4
Then I am getting this error
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/tmpd2xagkli/forward /tmp/tmpd2xagkli/reverse /tmp/tmpd2xagkli/output.tsv.biom /tmp/tmpd2xagkli/track.tsv /tmp/tmpd2xagkli/filt_f /tmp/tmpd2xagkli/filt_r 150 140 20 20 2.0 2 consensus 1.0 4 1000000
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
1) Filtering ..........
2) Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 159 reads in 159 unique sequences.
Sample 2 - 161 reads in 161 unique sequences.
Sample 3 - 165 reads in 165 unique sequences.
Sample 4 - 168 reads in 168 unique sequences.
Sample 5 - 157 reads in 157 unique sequences.
Sample 6 - 158 reads in 158 unique sequences.
Sample 7 - 160 reads in 160 unique sequences.
Sample 8 - 178 reads in 178 unique sequences.
Sample 9 - 163 reads in 163 unique sequences.
Sample 10 - 145 reads in 145 unique sequences.
selfConsist step 2
Convergence after 2 rounds.
2b) Reverse Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 159 reads in 159 unique sequences.
Sample 2 - 161 reads in 161 unique sequences.
Sample 3 - 165 reads in 165 unique sequences.
Sample 4 - 168 reads in 168 unique sequences.
Sample 5 - 157 reads in 157 unique sequences.
Sample 6 - 158 reads in 158 unique sequences.
Sample 7 - 160 reads in 160 unique sequences.
Sample 8 - 178 reads in 178 unique sequences.
Sample 9 - 163 reads in 163 unique sequences.
Sample 10 - 145 reads in 145 unique sequences.
selfConsist step 2
Convergence after 2 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/ashutosh/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 231, in denoise_paired
run_commands([cmd])
File "/home/ashutosh/anaconda2/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/ashutosh/anaconda2/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/tmpd2xagkli/forward', '/tmp/tmpd2xagkli/reverse', '/tmp/tmpd2xagkli/output.tsv.biom', '/tmp/tmpd2xagkli/track.tsv', '/tmp/tmpd2xagkli/filt_f', '/tmp/tmpd2xagkli/filt_r', '150', '140', '20', '20', '2.0', '2', 'consensus', '1.0', '4', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ashutosh/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "</home/ashutosh/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-442>", line 2, in denoise_paired
File "/home/ashutosh/anaconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/ashutosh/anaconda2/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/ashutosh/anaconda2/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.
Can you suggest what wrong with my files or command?
Thanks in advance