Example: 200 barcodes, asymmetric mode (try each barcode forward and reverse-complement), 300,000 CCS reads. On my 2014 iMac with 4 cores + HT:
503.57s user 11.74s system 725% cpu 1:11.01 total
Those 1:11 minutes translate into 0.233 milliseconds per ZMW, 1.16 microseconds per barcode for both sides aligning forward and reverse-complement, and 291 nanoseconds per alignment. This includes IO.
This might be a simple IO bottleneck. With a barcode.fasta containing only a few barcodes, most of the time is spent reading and writing BAM files, as the barcode identification is too fast. Starting version 2.2.0, you can enable multi-threaded BAM reading by setting the number of threads via an environment variable
No. Please run
wc -l prefix.report to get the number of already processed ZMWs.