Dear qiime2 staff.
I got an error when using dada2 to denoise a double-ended sequencing sequence: Plugin error from dada2: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
I see multiple problems similar to mine in the forum, but there is no helpful solution at the moment.
I'll start by describing the data I used, I identified a portion of the data of interest from the literature and hopefully I can re-analyze this data myself, they used 338F and 806R for amplification of the V3-V4 region, Illumina MiSeq PE300 sequencing.
Here is the base mass distribution of this pair-end sequencing set：
Next I used dada for noise reduction of the sequences (the splice sequences, primers have been removed using trimmomatic before data import).
time qiime dada2 denoise-paired
I got an error report and I tried to change the truncation location, most of them are repeating this error:
I monitored the running process and found that there was an error in the calculation of removing the chimeras and the sequence table was not generated, the following is the test log:
I continued to try, and I saw that there was a claim that the two bit truncation lengths needed to add up to a certain threshold, and I adjusted the parameter to --p-trunc-len-f 260
--p-trunc-len-r 220; found that it ran successfully, but the dada2_stats result showed that it could not be spliced after successful filtering, so obviously this was a failed attempt. I would like to know if there is an error in my whole processing process that I am not aware of, or if this data set is not suitable for processing with DADA, and look forward to your reply.
Unfortunately the pair-end.qza file exceeds the size limit, I can provide it in other ways if needed.