Hello,
I have been getting the following error after the denoising step:
(Plugin 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-n3qt2be9.log)
I use this command:
((qiime2-2019.4) richardliu@richardliu:~/qiime2-atacama-tutorial$ qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trim-left-f 13 --p-trim-left-r 13 --p-trunc-len-f 150 --p-trunc-len-r 150 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza)
and this is the log:
(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/tmp3pinuyd0/forward /tmp/tmp3pinuyd0/reverse /tmp/tmp3pinuyd0/output.tsv.biom /tmp/tmp3pinuyd0/track.tsv /tmp/tmp3pinuyd0/filt_f /tmp/tmp3pinuyd0/filt_r 150 150 13 13 2.0 2 consensus 1.0 1 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.1 / RcppParallel: 4.4.2
- Filtering The filter removed all reads: /tmp/tmp3pinuyd0/filt_f/YUN2029.3_65_L001_R1_001.fastq.gz and /tmp/tmp3pinuyd0/filt_r/YUN2029.3_65_L001_R2_001.fastq.gz not written.
Some input samples had no reads pass the filter.
...........................................x............................... - Learning Error Rates
57982099 total bases in 423227 reads from 74 samples will be used for learning the error rates.
Traceback (most recent call last):
File "/home/richardliu/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 231, in denoise_paired
run_commands([cmd])
File "/home/richardliu/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/richardliu/miniconda3/envs/qiime2-2019.4/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp3pinuyd0/forward', '/tmp/tmp3pinuyd0/reverse', '/tmp/tmp3pinuyd0/output.tsv.biom', '/tmp/tmp3pinuyd0/track.tsv', '/tmp/tmp3pinuyd0/filt_f', '/tmp/tmp3pinuyd0/filt_r', '150', '150', '13', '13', '2.0', '2', 'consensus', '1.0', '1', '1000000']' died with <Signals.SIGKILL: 9>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/richardliu/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py", line 311, in call
results = action(**arguments)
@@@
"/tmp/qiime2-q2cli-err-n3qt2be9.log" 36L, 2907C 1,1 Top
)
It would be great if anyone could guide me.
The qiime 2 version that am using is qiime2 2019.04
and the data is from “Atacama soil microbiome” tutorial — QIIME 2 2019.4.0 documentation
@will @MSullivan @jairideout @thermokarst
