Dear QIIME2 support team,
I am running QIIME2 on a data set of demultiplexed paired end reads. I am having this error persistently now: It begun when I brought together fastq files from 2 separate runs with different identities:
The last error log was:
less /tmp/qiime2-q2cli-err-69szp22i.log
Mismatched forward and reverse sequence files: 100000, 39538.
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/tmpqmwoe_2q/forward /tmp/tmpqmwoe_2q/reverse /tmp/tmpqmwoe_2q/output.tsv.biom /tmp/tmpqmwoe_2q/track.tsv /tmp/tmpqmwoe_2q/filt_f /tmp/tmpqmwoe_2q/filt_r 120 120 0 0 2.0 2 consensus 1.0 1 1000000
Traceback (most recent call last):
File “/export/apps/qiime2/2018.4/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/export/apps/qiime2/2018.4/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/export/apps/qiime2/2018.4/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpqmwoe_2q/forward’, ‘/tmp/tmpqmwoe_2q/reverse’, ‘/tmp/tmpqmwoe_2q/output.tsv.biom’, ‘/tmp/tmpqmwoe_2q/track.tsv’, ‘/tmp/tmpqmwoe_2q/filt_f’, ‘/tmp/tmpqmwoe_2q/filt_r’, ‘120’, ‘120’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned n/tmp/qiime2-q2cli-err-69szp22i.log.
What is the best way to share my fastq files and metadata file so as to help me assess there is no problem with these two files?
On my end I have done a thorough check and I am turning nothing, yet when I run DADA2, the same error is generated.
Thanks for your kind regard,
Ben.