I need help with the command for dada2 of an ITS data. After trimming the paired-end sequences with itsexpress, I encountered this error:
Plugin error from dada2:
No reads passed the filter. trunc_len_f (0) or trunc_len_r (0) may be individually longer than read lengths, or trunc_len_f + trunc_len_r may be shorter than the length of the amplicon + 12 nucleotides (the length of the overlap). Alternatively, other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.
Debug info has been saved to /tmp/qiime2-q2cli-err-xxd57hwb.log
GNU nano 4.8 /tmp/qiime2-q2cli-err-gw2qi0do.log
Running external command-line application(s). This may print messages to stdou>
The command(s) being run are below. These commands cannot be manually re-run a>
R version 4.0.2 (2020-06-22)
Loading required package: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.5 / RcppParallel: 5.0.2
Filtering The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/101A_8_L001>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/101B_6_L001_R1_001.fastq>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/101C_9_L001_R1_001.fastq>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/202A_1_L001_R1_001.fastq>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/202B_11_L001_R1_001.fast>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/202C_4_L001_R1_001.fastq>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/303A_7_L001_R1_001.fastq>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/303B_12_L001_R1_001.fast>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/303C_3_L001_R1_001.fastq>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/404A_2_L001_R1_001.fastq>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/404B_10_L001_R1_001.fast>
The filter removed all reads: /tmp/tmpu52d3lx0/filt_f/404C_5_L001_R1_001.fastq>
Error: No reads passed the filter (were truncLenF/R longer than the read lengt>
Traceback (most recent call last):
I don't know why all the reads were reduced so much.
I realised from my demux-details.qza that my reads look trimmed and neat.
What is the implication of that? (Someone told me that sequencing reads from Illumina facility/MRDNA are quality trimmed and they are not so good with dada2 but that I should use deblur, I haven't tried that before)
Could this be the reason for the above error?
You asked us above why your read count was reduced:
Then you shared the following list of filenames:
Unfortunately we can't do anything with the filenames (or those file disk sizes). It looks like you tried attaching files here for us to review and they weren't successfully attached, that's why I was asking for you to try again. Let me know if you need help with that!