lima ERROR: [pbcopper] alarm ERROR: cannot write to empty alarm filename

[kenneditodd]

Hello,

I am using the command line version of smrtlink 13.1.

I have a sample prepped for Iso-Seq using SMRTbell prep kit 3.0. I was given the barcodes used by the sequencing core and I am now trying to run lima on a hifi_reads.bam file. I used the command below. lima --isoseq --peek-guess sample.hifi_reads.bam barcodes.fa sample.fl.bam However, I keep getting the error message below. | 20240417 18:19:20.804 | FATAL | lima ERROR: [pbcopper] alarm ERROR: cannot write to empty alarm filename

I noticed I can run lima if I remove the --peek-guess option. I tried this and don't get an output bam file. Below is my report. It seems 100% is below the min ref span.

ZMWs input                (A) : 5214513
ZMWs above all thresholds (B) : 0 (0.00%)
ZMWs below any threshold  (C) : 5214513 (100.00%)

ZMW marginals for (C):
Below min length              : 2 (0.00%)
Below min score               : 0 (0.00%)
Below min end score           : 470986 (9.03%)
Below min passes              : 0 (0.00%)
Below min score lead          : 0 (0.00%)
Below min ref span            : 5214513 (100.00%)
Without SMRTbell adapter      : 0 (0.00%)
Undesired 5p--5p pairs        : 182006 (3.49%)
Undesired 3p--3p pairs        : 146092 (2.80%)

ZMWs for (B):
Coefficient of correlation    : -nan%

ZMWs for (A):
Allow diff pair               : 5214513 (100.00%)
Allow same pair               : 5214513 (100.00%)

Reads for (B):
Above length                  : 0 (-nan%)
Below length                  : 0 (-nan%)

Is someone able to help in the issue i'm having with --peek-guess and/or why none of my reads pass? @armintoepfer