This is the log for dada2 run for last batch of sequenced samples without showing previous error in older sequenced samples.
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
1) Filtering .....................................................................................................
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.
2) Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 39194 reads in 18072 unique sequences.
Sample 2 - 44820 reads in 14200 unique sequences.
Sample 3 - 95965 reads in 34938 unique sequences.
Sample 4 - 49969 reads in 20767 unique sequences.
Sample 5 - 63438 reads in 19303 unique sequences.
Sample 6 - 62350 reads in 18530 unique sequences.
Sample 7 - 49340 reads in 18911 unique sequences.
Sample 8 - 60695 reads in 22343 unique sequences.
Sample 9 - 77311 reads in 22536 unique sequences.
Sample 10 - 64340 reads in 25432 unique sequences.
Sample 11 - 44313 reads in 16861 unique sequences.
Sample 12 - 59871 reads in 22531 unique sequences.
Sample 13 - 73882 reads in 32930 unique sequences.
Sample 14 - 59350 reads in 23047 unique sequences.
Sample 15 - 23171 reads in 8916 unique sequences.
Sample 16 - 70327 reads in 29284 unique sequences.
Sample 17 - 59912 reads in 20902 unique sequences.
Sample 18 - 31603 reads in 13802 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
selfConsist step 7
selfConsist step 8
selfConsist step 9
selfConsist step 10
Self-consistency loop terminated before convergence.
2b) Reverse Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 39194 reads in 22616 unique sequences.
Sample 2 - 44820 reads in 20319 unique sequences.
Sample 3 - 95965 reads in 49275 unique sequences.
Sample 4 - 49969 reads in 26094 unique sequences.
Sample 5 - 63438 reads in 29221 unique sequences.
Sample 6 - 62350 reads in 29065 unique sequences.
Sample 7 - 49340 reads in 26150 unique sequences.
Sample 8 - 60695 reads in 31435 unique sequences.
Sample 9 - 77311 reads in 30663 unique sequences.
Sample 10 - 64340 reads in 33927 unique sequences.
Sample 11 - 44313 reads in 22315 unique sequences.
Sample 12 - 59871 reads in 30972 unique sequences.
Sample 13 - 73882 reads in 40548 unique sequences.
Sample 14 - 59350 reads in 30319 unique sequences.
Sample 15 - 23171 reads in 12529 unique sequences.
Sample 16 - 70327 reads in 37462 unique sequences.
Sample 17 - 59912 reads in 28615 unique sequences.
Sample 18 - 31603 reads in 18769 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
selfConsist step 7
Convergence after 7 rounds.
3) Denoise remaining samples ......................................................................................................................................................................................................
The sequences being tabled vary in length.
4) Remove chimeras (method = consensus)
input filtered denoised merged non-chimeric
A001w28_0_L001_R1_001.fastq.gz 73992 39194 39194 389 285
A002w28_2_L001_R1_001.fastq.gz 87635 44820 44820 88 87
A003w28_4_L001_R1_001.fastq.gz 187455 95965 95965 243 235
A004w28_6_L001_R1_001.fastq.gz 89517 49969 49969 18 16
A005w28_8_L001_R1_001.fastq.gz 115993 63438 63438 44 44
A006w28_10_L001_R1_001.fastq.gz 129567 62350 62350 28 28
6) Write output
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/tmpa1f97v01/forward /tmp/tmpa1f97v01/reverse /tmp/tmpa1f97v01/output.tsv.biom /tmp/tmpa1f97v01/filt_f /tmp/tmpa1f97v01/filt_r 222 222 0 0 2.0 2 consensus 1.0 0 1000000
Saved FeatureTable[Frequency] to: table-dada2_paired_w28.qza
Saved FeatureData[Sequence] to: rep-seqs-dada2_paired_w28.qza
Is this related specifically to issue in samples sequencing from the facility?