iss is skipping certain contigs during simulation

[tslaird]

Hi,

I'm trying to simulate reads from a genome (Pseudomonas_aeruginosa_ATCC_9027.fna : https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/601/815/GCF_002601815.1_ASM260181v1/GCF_002601815.1_ASM260181v1_genomic.fna.gz) which has 56 contigs.

I am running the command:

iss generate --draft Pseudomonas_aeruginosa_ATCC_9027.fna --output Pseudomonas_aeruginosa_ATCC_9027_resimulate4 --n_reads 100000 --mode kde --model hiSeq --seed 23 --coverage uniform --cpus 2 --debug

The simulation debug output is:

DEBUG:iss.app:iss version 2.0.1
DEBUG:iss.app:Using verbose logger
INFO:iss.app:Starting iss generate
INFO:iss.generator:Using kde ErrorModel
INFO:iss.generator:Setting random seed to 23
DEBUG:iss.error_models.kde.KDErrorModel:Loaded ErrorProfile: /home/tyler/miniforge3/envs/insilicoseq/lib/python3.12/site-packages/iss/profiles/HiSeq
INFO:iss.util:Stitching input files together
INFO:iss.generator:Using uniform coverage distribution
INFO:iss.generator:scaling coverage to 100000 reads
INFO:iss.app:Using 2 cpus for read generation
INFO:iss.app:Generating 100000 reads
DEBUG:iss.app:Chunk size: 25000
DEBUG:iss.generator:Will generate 5131 read pairs for NZ_NIQD01000010.1
DEBUG:iss.generator:Adding a pair to correct rounding error
DEBUG:iss.generator:Will generate 4573 read pairs for NZ_NIQD01000011.1
DEBUG:iss.generator:Will generate 3760 read pairs for NZ_NIQD01000012.1
DEBUG:iss.generator:Will generate 3656 read pairs for NZ_NIQD01000013.1
DEBUG:iss.generator:Will generate 3559 read pairs for NZ_NIQD01000014.1
DEBUG:iss.generator:Will generate 3090 read pairs for NZ_NIQD01000015.1
DEBUG:iss.generator:Will generate 2704 read pairs for NZ_NIQD01000016.1
DEBUG:iss.generator:Will generate 2538 read pairs for NZ_NIQD01000017.1
DEBUG:iss.generator:Will generate 1685 read pairs for NZ_NIQD01000018.1
DEBUG:iss.generator:Will generate 1527 read pairs for NZ_NIQD01000019.1
DEBUG:iss.generator:Will generate 9524 read pairs for NZ_NIQD01000001.1
DEBUG:iss.generator:Will generate 1240 read pairs for NZ_NIQD01000020.1
DEBUG:iss.generator:Will generate 1058 read pairs for NZ_NIQD01000021.1
DEBUG:iss.generator:Will generate 321 read pairs for NZ_NIQD01000022.1
DEBUG:iss.generator:Will generate 228 read pairs for NZ_NIQD01000023.1
DEBUG:iss.generator:Will generate 88 read pairs for NZ_NIQD01000024.1
DEBUG:iss.generator:Will generate 82 read pairs for NZ_NIQD01000025.1
DEBUG:iss.generator:Will generate 56 read pairs for NZ_NIQD01000026.1
DEBUG:iss.generator:Will generate 38 read pairs for NZ_NIQD01000027.1
DEBUG:iss.generator:Will generate 22 read pairs for NZ_NIQD01000028.1
DEBUG:iss.generator:Will generate 19 read pairs for NZ_NIQD01000029.1
DEBUG:iss.generator:Adding a pair to correct rounding error
DEBUG:iss.generator:Will generate 7948 read pairs for NZ_NIQD01000002.1
DEBUG:iss.generator:Will generate 16 read pairs for NZ_NIQD01000030.1
DEBUG:iss.generator:Will generate 15 read pairs for NZ_NIQD01000031.1
DEBUG:iss.generator:Will generate 13 read pairs for NZ_NIQD01000032.1
DEBUG:iss.generator:Will generate 8 read pairs for NZ_NIQD01000033.1
DEBUG:iss.generator:Will generate 11 read pairs for NZ_NIQD01000034.1
DEBUG:iss.generator:Will generate 9 read pairs for NZ_NIQD01000035.1
DEBUG:iss.generator:Will generate 7696 read pairs for NZ_NIQD01000003.1
DEBUG:iss.generator:Will generate 7 read pairs for NZ_NIQD01000036.1
DEBUG:iss.generator:Will generate 6 read pairs for NZ_NIQD01000037.1
DEBUG:iss.generator:Will generate 6 read pairs for NZ_NIQD01000038.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000039.1
DEBUG:iss.generator:Adding a pair to correct rounding error
DEBUG:iss.generator:Will generate 5 read pairs for NZ_NIQD01000040.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000041.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000042.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000043.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000044.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000045.1
DEBUG:iss.generator:Will generate 7662 read pairs for NZ_NIQD01000004.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000046.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000047.1
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000048.1
DEBUG:iss.generator:Will generate 3 read pairs for NZ_NIQD01000049.1
DEBUG:iss.generator:Will generate 3 read pairs for NZ_NIQD01000050.1
DEBUG:iss.generator:Will generate 3 read pairs for NZ_NIQD01000051.1
DEBUG:iss.generator:Will generate 3 read pairs for NZ_NIQD01000052.1
DEBUG:iss.generator:Will generate 3 read pairs for NZ_NIQD01000053.1
DEBUG:iss.generator:Will generate 3 read pairs for NZ_NIQD01000054.1
DEBUG:iss.generator:Adding a pair to correct rounding error
DEBUG:iss.generator:Will generate 4 read pairs for NZ_NIQD01000055.1
DEBUG:iss.generator:Will generate 7222 read pairs for NZ_NIQD01000005.1
DEBUG:iss.generator:Cpu #0: Generating 5131 read pairs
DEBUG:iss.generator:Cpu #1: Generating 1473 read pairs
DEBUG:iss.generator:Cpu #1: Generating 2538 read pairs
DEBUG:iss.generator:Cpu #1: Generating 1685 read pairs
DEBUG:iss.generator:Cpu #0: Generating 4573 read pairs
DEBUG:iss.generator:Cpu #1: Generating 1527 read pairs
DEBUG:iss.generator:Cpu #1: Generating 9524 read pairs
DEBUG:iss.generator:Cpu #0: Generating 3760 read pairs
DEBUG:iss.generator:Cpu #0: Generating 3656 read pairs
DEBUG:iss.generator:Cpu #0: Generating 3559 read pairs
DEBUG:iss.generator:Cpu #1: Generating 1240 read pairs
DEBUG:iss.generator:Cpu #1: Generating 1058 read pairs
DEBUG:iss.generator:Cpu #1: Generating 321 read pairs
DEBUG:iss.generator:Cpu #1: Generating 228 read pairs
DEBUG:iss.generator:Cpu #1: Generating 88 read pairs
DEBUG:iss.generator:Cpu #1: Generating 82 read pairs
DEBUG:iss.generator:Cpu #1: Generating 56 read pairs
DEBUG:iss.generator:Cpu #1: Generating 38 read pairs
DEBUG:iss.generator:Cpu #1: Generating 22 read pairs
DEBUG:iss.generator:Cpu #1: Generating 19 read pairs
DEBUG:iss.generator:Cpu #1: Generating 5101 read pairs
DEBUG:iss.generator:Cpu #0: Generating 3090 read pairs
DEBUG:iss.generator:Cpu #0: Generating 1231 read pairs
INFO:iss.util:Stitching input files together
INFO:iss.util:Stitching input files together
INFO:iss.util:Cleaning up
INFO:iss.app:Read generation complete

First, there are only 51 contigs represented in the section where iss says "Will generate X read pairs ..."

Then there are only 23 actual lines that for the iss.generator:Cpu component

Then in the .vcf file there are only 22 contigs represented with errors.

When I map back the simulated reads to the whole genome using bowtie2 there are whole contigs that have no reads associated with them despite the coverage saying that all 56 contigs are covered a 3.96x

I have also tried this with 10 M reads and get the same thing. I have tried tweaking different parameters but am not sure why the contigs keep getting missed.

I have also moved some of the contigs around in the genome file and tried deleting some and that does change which contigs get represented but there is still missing contig representation in the output.

Hopefully you can troubleshoot this issue.

Thanks,

-Tyler-