Hi @nerdynella: We implemented an auto-logging feature in QIIME 2 2017.5:
When a command fails and is not in --verbose mode, the command's output is saved to a temporary log file. This is useful when errors take a while to trigger; users no longer have to rerun the command with --verbose (and wait) to see the full error message.
An example when run without --verbose:
$ qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza \
--o-table table \
--o-representative-sequences rep-seqs \
--p-trim-left-f 0 \
--p-trim-left-r 0 \
--p-trunc-len-f 300 \
--p-trunc-len-r 300 \
--p-n-threads 0
Plugin error from dada2:
Command '['run_dada_paired.R', '/var/folders/5y/k_d_lfy57pxbg3l7j_3r9y
sh0000gn/T/tmp6rkj5go1/forward', '/var/folders/5y/k_d_lfy57pxbg3l7j_3r
9ysh0000gn/T/tmp6rkj5go1/reverse', '/var/folders/5y/k_d_lfy57pxbg3l7j_
3r9ysh0000gn/T/tmp6rkj5go1/output.tsv.biom',
'/var/folders/5y/k_d_lfy57pxbg3l7j_3r9ysh0000gn/T/tmp6rkj5go1/filt_f',
'/var/folders/5y/k_d_lfy57pxbg3l7j_3r9ysh0000gn/T/tmp6rkj5go1/filt_r',
'300', '300', '0', '0', '2.0', '2', 'consensus', '1.0', '0',
'1000000']' returned non-zero exit status 1
Debug info has been saved to /var/folders/5y/k_d_lfy57pxbg3l7j_3r9ysh0000gn/T/qiime2-q2cli-err-4vorneiu.log.
The log file at /var/folders/5y/k_d_lfy57pxbg3l7j_3r9ysh0000gn/T/qiime2-q2cli-err-4vorneiu.log contains the same info you would see if you ran the command with --verbose (this file will be different for each run, and different on each computer)! It might be worth checking through your command line history or your temp directory to see if they are still hanging around.