0 readpairs per molecule

[pdimens]

Hello, I'm trying to run LRSIM on a drosophila genome and finding that it keeps saying that it's simulating 0 read pairs per molecule. Perhaps I'm putting in the wrong parameters, but I can't seem to determine what's going on. The genome is >100mb as recommended.

The runtime parameters are:

NUMREADS=1   # in millions
MOLLEN=80    # in kbp
MOLPER=5
NUMINV=50
NUMINDEL=0
SNPPER=200000
INVMIN=1000
INVMAX=10000
TRANSLOC=0
PARTITIONS=2500    # default: 1500
NUMTHREADS=8
outprefix="./1millionreads/sims"
BARCODES="barcodes-500M.txt"

./simulateLinkedReads.pl \
    -r dmel.trunc.noN.fa \
    -p $outprefix \
    -b $BARCODES \
    -x $NUMREADS \
    -f $MOLLEN \
    -m $MOLPER \
    -1 $SNPPER \
    -4 $NUMINDEL \
    -5 $INVMIN \
    -6 $INVMAX \
    -7 $NUMINV \
    -0 $TRANSLOC \
    -z $NUMTHREADS \
    -o

[dwgsim_core] 2L length: 23582449
[dwgsim_core] 2R length: 25422852
[dwgsim_core] 3L length: 28239365
[dwgsim_core] 3R length: 32150935
[dwgsim_core] 4 length: 1430978
[dwgsim_core] X length: 23654338
[dwgsim_core] Y length: 3765010
[dwgsim_core] 7 sequences, total length: 138245927
[dwgsim_core] Currently on:
[dwgsim_core] 187500
[dwgsim_core] Complete!
[dwgsim_core] 120000Thu Nov 30 11:50:31 2023: DWGSIM round 1 thread 1 end
[dwgsim_core] 187500
[dwgsim_core] Complete!
Thu Nov 30 11:50:33 2023: DWGSIM round 1 thread 2 end
[dwgsim_core] 70000Thu Nov 30 11:50:34 2023: cat ./1millionreads/sims.dwgsim.0.1.12.fastq >> ./1millionreads/sims.dwgsim.0.12.fastq
[dwgsim_core] 80000Thu Nov 30 11:50:34 2023: cat ./1millionreads/sims.dwgsim.0.2.12.fastq >> ./1millionreads/sims.dwgsim.0.12.fastq
Thu Nov 30 11:50:34 2023: cat ./1millionreads/sims.dwgsim.0.3.12.fastq >> ./1millionreads/sims.dwgsim.0.12.fastq
[dwgsim_core] 90000Thu Nov 30 11:50:34 2023: cat ./1millionreads/sims.dwgsim.1.1.12.fastq >> ./1millionreads/sims.dwgsim.1.12.fastq
Thu Nov 30 11:50:34 2023: cat ./1millionreads/sims.dwgsim.1.2.12.fastq >> ./1millionreads/sims.dwgsim.1.12.fastq
[dwgsim_core] 187500
[dwgsim_core] Complete!
Thu Nov 30 11:50:37 2023: DWGSIM round 1 thread 3 end
Thu Nov 30 11:50:37 2023: cat ./1millionreads/sims.dwgsim.1.3.12.fastq >> ./1millionreads/sims.dwgsim.1.12.fastq
Thu Nov 30 11:50:37 2023: Simulate reads start
Thu Nov 30 11:50:37 2023: Load barcodes start
Thu Nov 30 11:54:38 2023: Load barcodes end
Thu Nov 30 11:54:38 2023: readPairsPerMolecule: 0                    <----- THIS PART
Thu Nov 30 11:54:38 2023: Simulating on haplotype: 0
Thu Nov 30 11:54:38 2023: Load read positions haplotype 0
Thu Nov 30 11:54:41 2023: 0 reads failed being loaded.
Thu Nov 30 11:54:41 2023: Exporting ./1millionreads/sims.0.fp
Thu Nov 30 11:54:42 2023: Exported ./1millionreads/sims.0.fp
Thu Nov 30 11:54:42 2023: readsCountDown: 500000                 <------ NEVER MOVES PAST THIS PART