Troubleshooting

Demultiplexing with Guppy

Error:

Init time: 2515 ms

0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
Caller time: 32995 ms, Samples called: 159196780, samples/s: 4.82488e+06
Finishing up any open output files.
Basecalling completed successfully.

Command error:
rm: cannot remove '*_out/*/*.fastq': No such file or directory

Solution: Check your barcode kit!. You must indicate the –barcode_kits in the tool_opts file at the row demultiplexing guppy. Example:

demultiplexing guppy  "--flowcell FLO-MIN114 --kit SQK-LSK114 --barcode_kits SQK-NBD114-24"

Memory failures in mop_preprocess and mop_mod

Sometimes FastQC, Epinano, or other tools can run out of memory because the input data contain low-quality reads. It is always a good idea to double-check it and eventually filter them per size / quality using either nanoq or nanofilt.