Hello, I have imported the data into QIIME2 as demux.qzv,
I've use this command to summarize the data:
qiime demux summarize
--i-data demux.qza
--o-visualization demux.qzv
(demux.qzv renamed as ZIP)
demux.zip (322.7 KB)
###I've checked all the forward & reverse sequence count by R, they are all the same.
Then I use this command to generate feature tables and representative sequences:
time qiime dada2 denoise-paired
--i-demultiplexed-seqs demux.qza
--p-n-threads 32
--p-trim-left-f 0 --p-trim-left-r 0
--p-trunc-len-f 0 --p-trunc-len-r 0
--o-table dada2-table.qza
--o-representative-sequences dada2-rep-seqs.qza
--o-denoising-stats denoising-stats.qza
Still, I got that error message:
R version 4.0.2 (2020-06-22)
Loading required package: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.6 / RcppParallel: 5.0.2
- Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, :
These are the errors (up to 5) encountered in individual cores...
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 4548, 100000.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 100000, 4548.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 4548, 100000.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 100000, 4548.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 4548, 100000.
Execution halted
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/tmpd583su6s/forward /tmp/tmpd583su6s/reverse /tmp/tmpd583su6s/output.tsv.biom /tmp/tmpd583su6s/track.tsv /tmp/tmpd583su6s/filt_f /tmp/tmpd583su6s/filt_r 0 0 0 0 2.0 2.0 2 independent consensus 1.0 32 1000000
Traceback (most recent call last):
File "/home/disk/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 264, in denoise_paired
run_commands([cmd])
File "/home/disk/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/disk/.conda/envs/qiime2-2021.2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpd583su6s/forward', '/tmp/tmpd583su6s/reverse', '/tmp/tmpd583su6s/output.tsv.biom', '/tmp/tmpd583su6s/track.tsv', '/tmp/tmpd583su6s/filt_f', '/tmp/tmpd583su6s/filt_r', '0', '0', '0', '0', '2.0', '2.0', '2', 'independent', 'consensus', '1.0', '32', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/disk/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/disk/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/disk/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/disk/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 279, 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.
My QIIME2 version is 2021.2, installed via conda
I have no idea what's going wrong...
PLEASE help me to find out how to solve it, thank you very much!