Hello,
I get the following error when I try to run DADA2.
(qiime2-2017.11) Ginas-MacBook-Pro-2:BigBend ginacerbie$ qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux3.qza
--p-trim-left-f 13
--p-trim-left-r 13
--p-trunc-len-f 150
--p-trunc-len-r 150
--o-representative-sequences rep-seqs.qza
--o-table table.qza --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 /var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/forward /var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/reverse /var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/output.tsv.biom /var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/filt_f /var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/filt_r 150 150 13 13 2.0 2 consensus 1.0 1 1000000
R version 3.3.2 (2016-10-31)
Loading required package: Rcpp
There were 50 or more warnings (use warnings() to see the first 50)
DADA2 R package version: 1.4.0
- Filtering ....................................................Error in fastqPairedFilter(c(unfiltsF[[i]], unfiltsR[[i]]), c(filteredFastqF, :
Mismatched forward and reverse sequence files: 78418, 78417.
Execution halted
Traceback (most recent call last):
File "/Users/ginacerbie/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/Users/ginacerbie/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/Users/ginacerbie/miniconda3/envs/qiime2-2017.11/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/forward', '/var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/reverse', '/var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/output.tsv.biom', '/var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/filt_f', '/var/folders/1z/j61p4k6d079f7rnvw63s0mnm0000gn/T/tmpr1fjj6dz/filt_r', '150', '150', '13', '13', '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/ginacerbie/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/q2cli/commands.py", line 218, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/Users/ginacerbie/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 220, in bound_callable
output_types, provenance)
File "/Users/ginacerbie/miniconda3/envs/qiime2-2017.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 355, in callable_executor
output_views = self._callable(**view_args)
File "/Users/ginacerbie/miniconda3/envs/qiime2-2017.11/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 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.
I thought the following "Mismatched forward and reverse sequence files: 78418, 78417" was odd. In the other forum posts regarding this topic, I noticed that those numbers were more than one off. Any ideas on what might be causing this mismatch?
My manifest file is attached below but I was not able to find any naming errors.
AmphipodManifest.csv (9.8 KB)
In case it helps, I used the following to import the data:
(qiime2-2017.11) Ginas-MacBook-Pro-2:BigBend ginacerbie$ qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path AmphipodManifest.csv
--output-path paired-end-demux3.qza
--source-format PairedEndFastqManifestPhred33
Thank you so much!
Gina