Hello everyone!
I download public suquences from NCBI. After importing the data through fastq manifest way I get the paired-end-demux.qza to perform dada2 denoising.
But I face the problem in this step. Here is my executive code and the error report.
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trim-left-f 13 --p-trim-left-r 13 --p-trunc-len-f 244 --p-trunc-len-r 189 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 0 --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/tmps_ld6lyi/forward /tmp/tmps_ld6lyi/reverse /tmp/tmps_ld6lyi/output.tsv.biom /tmp/tmps_ld6lyi/track.tsv /tmp/tmps_ld6lyi/filt_f /tmp/tmps_ld6lyi/filt_r 244 189 13 13 2.0 2 consensus 1.0 0 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 - 45467 reads in 11282 unique sequences.
Sample 2 - 39922 reads in 10004 unique sequences.
Sample 3 - 34691 reads in 8795 unique sequences.
Sample 4 - 39821 reads in 9593 unique sequences.
Sample 5 - 46728 reads in 10118 unique sequences.
Sample 6 - 43315 reads in 8886 unique sequences.
Sample 7 - 33738 reads in 9808 unique sequences.
Sample 8 - 41172 reads in 6750 unique sequences.
Sample 9 - 37529 reads in 7488 unique sequences.
Sample 10 - 47771 reads in 8572 unique sequences.
Sample 11 - 35831 reads in 7253 unique sequences.
Sample 12 - 31295 reads in 7694 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
Convergence after 5 rounds.
2b) Reverse Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 45467 reads in 9951 unique sequences.
Sample 2 - 39922 reads in 8259 unique sequences.
Sample 3 - 34691 reads in 7112 unique sequences.
Sample 4 - 39821 reads in 8103 unique sequences.
Sample 5 - 46728 reads in 9504 unique sequences.
Sample 6 - 43315 reads in 6603 unique sequences.
Sample 7 - 33738 reads in 10081 unique sequences.
Sample 8 - 41172 reads in 4582 unique sequences.
Sample 9 - 37529 reads in 5530 unique sequences.
Sample 10 - 47771 reads in 7667 unique sequences.
Sample 11 - 35831 reads in 6742 unique sequences.
Sample 12 - 31295 reads in 6762 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
Convergence after 6 rounds. -
Denoise remaining samples
-
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/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 231, in denoise_paired
run_commands([cmd])
File "/home/qiime2/miniconda/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/qiime2/miniconda/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/tmps_ld6lyi/forward', '/tmp/tmps_ld6lyi/reverse', '/tmp/tmps_ld6lyi/output.tsv.biom', '/tmp/tmps_ld6lyi/track.tsv', '/tmp/tmps_ld6lyi/filt_f', '/tmp/tmps_ld6lyi/filt_r', '244', '189', '13', '13', '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 "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "</home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-442>", line 2, in denoise_paired
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/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/qiime2/miniconda/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.
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.
It seems that the memory in my device is limited. But I am sure I give enough memory to execute these data. So why qiime2 aborted in the final step?
this is the data which I got from NCBI and I split the paired-end sequence to two files.
