Hi,
Is it the same problem as mentioned above? Is there a way to fix it? Please have a look on command I have used and the error I got. Thanks in advance!
PS C:\Users\ha1254ke\KHH006_Analysis> docker run -t -i -v C:\Users\ha1254ke\KHH006_Analysis:/data qiime2/core:2017.7 qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --o-table table --o-representative-sequences rep-seqs --p-trim-left-f 6 --p-trim-left-r 7 --p-trunc-len-f 300 --p-trunc-len-r 192
e[31me[1mPlugin error from dada2:
An error was encountered while running DADA2 in R (return code -9),
please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-_olzv864.log.e[0m
Hi,
Thank you for the reply!
Since I am new to Docker, it will probably take me more time to figure out how to extract log files from a docker container! I will get back to you as soon as the log file is extracted.
PS C:\Users\ha1254ke\KHH006_Analysis> docker run -t -i -v C:\Users\ha1254ke\KHH006_Analysis:/data qiime2/core:2017.7 qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --o-table table --o-representative-sequences rep-seqs --p-trim-left-f 6 --p-trim-left-r 7 --p-trunc-len-f 300 --p-trunc-len-r 192 --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/tmpiz6h5ne4/forward /tmp/tmpiz6h5ne4/reverse /tmp/tmpiz6h5ne4/output.tsv.biom /tmp/tmpiz6h5ne4/filt_f /tmp/tmpiz6h5ne4/filt_r 300 192 6 7 2.0 2 consensus 1.0 1 1000000
R version 3.3.1 (2016-06-21)
Loading required package: Rcpp
Warning messages:
1: multiple methods tables found for ‘arbind’
2: multiple methods tables found for ‘acbind’
3: replacing previous import ‘IRanges::arbind’ by ‘SummarizedExperiment::arbind’ when loading ‘GenomicAlignments’
4: replacing previous import ‘IRanges::acbind’ by ‘SummarizedExperiment::acbind’ when loading ‘GenomicAlignments’
5: multiple methods tables found for ‘left’
6: multiple methods tables found for ‘right’
DADA2 R package version: 1.4.0
1) Filtering Traceback (most recent call last):
File "/opt/conda/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/opt/conda/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/opt/conda/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpiz6h5ne4/forward', '/tmp/tmpiz6h5ne4/reverse', '/tmp/tmpiz6h5ne4/output.tsv.biom', '/tmp/tmpiz6h5ne4/filt_f', '/tmp/tmpiz6h5ne4/filt_r', '300', '192', '6', '7', '2.0', '2', 'c
onsensus', '1.0', '1', '1000000']' returned non-zero exit status -9
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/lib/python3.5/site-packages/q2cli/commands.py", line 222, in __call__
results = action(**arguments)
File "<decorator-gen-126>", line 2, in denoise_paired
File "/opt/conda/lib/python3.5/site-packages/qiime2/sdk/action.py", line 201, in callable_wrapper
output_types, provenance)
File "/opt/conda/lib/python3.5/site-packages/qiime2/sdk/action.py", line 334, in _callable_executor_
output_views = callable(**view_args)
File "/opt/conda/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 -9), please inspect stdout and stderr to learn more.
e[31me[1mPlugin error from dada2:
An error was encountered while running DADA2 in R (return code -9),
please inspect stdout and stderr to learn more.
See above for debug info.e[0m
I'm having the exact the same error log as originally posted here and wanted to clarify.
By input files do you just mean the single paired-end-demux.qza file?
Also, is there a way to check that this artifact has been created properly and is in the appropriate format for dada2? I noticed that this input artifact (~3GB) wouldn't show on qiime2-view, however my demux-summary.qzv artifact shows the interactive plots just fine.
Turns out the error was related to insufficient memory in my dedicated partition. There was less than 1 Gig left in my partition and so just creating some space solved the issue.
Hi Ben,
I hope you will excuse me for the late reply. I was on parental leave to take care of my new baby!
I have checked the input files and I think they are in the appropriate format.
On the other hand, the RAM assigned for the VM (Docker) was 2GB. Based on the suggestion given above, I have increased the RAM allocated for Docker to 8GB and now the script is running for almost 1 hr which was not the case previously. Hope this will solve the problem.