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How fast is fast?

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.

Why doesn’t lima utilize the maximum number of provided cores?

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

export PB_BAMREADER_THREADS=2

Is there a way to show the progress?

No. Please run wc -l prefix.report to get the number of already processed ZMWs.


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