Error message: Can't find files for block a expected files such as

[Amanda-Biocortex]

Hi,

Im getting a DADA2 error message when running lotus2 (DADA2 + lambda) on some paired reads. Ive pasted some of the log output below. One thing I noticed was that pair2 is being trimmed at a very high precent value (the in the example below its 6.49042e+06% end - trimmed.

At ERR36_1.fastq:

Writing demultiplexed files to : ./lotus2/err/output//tmpFiles//demultiplexed/
50.5841% of 66175 reads accepted (99.0812% end-trimmed)
Pair 2: 6.49042e+06% of 66174 reads accepted (6.49042e+06% end - trimmed)
...

Reads processed: 5,374,129; 5,374,306 (pair 1;pair 2)
Rejected: 3,177,307; 5,374,763
Accepted (High qual): 2,197,369; 0 (64,093; 5,374,738 end-trimmed)
Accepted (Mid qual): 340;0
Singletons among these: 0; 0
Bad Reads recovered with dereplication: 2,072,433
Min/Avg/Max stats Pair 1
- sequence Length : 200/200/200
- Quality : 32/36.2312/38
- Median sequence Length : 0, Quality : 0
- Accum. Error 0.202734
Trimmed due to:

25 avg qual_ in 20 bp windows : 0; 0
(0.95) acc. errors, trimmed seqs : 0; 0
Rejected due to:
< min Sequence length (200) : 2,847,795; 5,374,741
-after Quality trimming : 2,847,692; 5,374,745
< avg Quality (27) : 0; 0
< window (50 nt) avg. Quality (25) : 27,259; 0
max Sequence length (1000) : 0; 0
(8) homo-nt run : 1,599; 0
(0) amb. Bases : 196; 0
(2.7) binomial est. errors : 327,807; 0
Specific sequence searches:
-With fwd Primer remaining (<= 0 mismatches) : 0; 0
-Barcode unidentified (max 0 errors) : 0

SampleID Barcode Instances
SMPL0 70,658
SMPL1 51,257
...

Error: Can't find files for block a expected files such as

Aborting dada2 run
Execution halted

Any help on this error message comes up would be greatly appreciated

[hildebra]

Hey Amanda,
pair 2 was completely rejected (0 reads passed) and I think this led to dada2 errors then:
"Reads processed: 5,374,129; 5,374,306 (pair 1;pair 2)
Rejected: 3,177,307; 5,374,763
Accepted (High qual): 2,197,369; 0 (64,093; 5,374,738 end-trimmed)"
all these seemed to be removed due to low quality:
"< min Sequence length (200) : 2,847,795; 5,374,741
"

really a bit unusual, was this normal illumina miSeq?