Illegal division by zero at /usr/local/bin/shovill line 162.

[xiaoli-dong]

We are using shovill for our project and it works great in most of the cases. When the sample do not have enough reads, it gives the "Illegal division by zero at /usr/local/bin/shovill line 162." error.

I am wondering whether shovill can exit nicely instead of just give the errors? See below the detail log:

[shovill] You ran: /usr/local/bin/shovill --R1 SC18-6016-A.dehost.R1.fastq.gz --R2 SC18-6016-A.dehost.R2.fastq.gz --assembler spades --minlen 300 --nocorr --cpus 6 --ram 24 --outdir ./ --force
[shovill] This is shovill 1.1.0
[shovill] Written by Torsten Seemann
[shovill] Homepage is https://github.com/tseemann/shovill
[shovill] Operating system is linux
[shovill] Perl version is v5.26.2
[shovill] Machine has 12 CPU cores and 62.39 GB RAM
[shovill] Using bwa - /usr/local/bin/bwa | Version: 0.7.17-r1188
[shovill] Using flash - /usr/local/bin/flash | FLASH v1.2.11
[shovill] Using java - /usr/local/bin/java | openjdk version "11.0.1" 2018-10-16 LTS
[shovill] Using kmc - /usr/local/bin/kmc | K-Mer Counter (KMC) ver. 3.1.1 (2019-05-19)
[shovill] Using lighter - /usr/local/bin/lighter | Lighter v1.1.2
[shovill] Using megahit - /usr/local/bin/megahit | MEGAHIT v1.2.9
[shovill] Using megahit_toolkit - /usr/local/bin/megahit_toolkit | v1.2.9
[shovill] Using pigz - /usr/local/bin/pigz | pigz 2.6
[shovill] Using pilon - /usr/local/bin/pilon | Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
[shovill] Using samclip - /usr/local/bin/samclip | samclip 0.4.0
[shovill] Using samtools - /usr/local/bin/samtools | Version: 1.13 (using htslib 1.13)
[shovill] Using seqtk - /usr/local/bin/seqtk | Version: 1.3-r106
[shovill] Using skesa - /usr/local/bin/skesa | SKESA 2.4.0
[shovill] Using spades.py - /usr/local/bin/spades.py | SPAdes genome assembler v3.14.1
[shovill] Using trimmomatic - /usr/local/bin/trimmomatic | 0.39
[shovill] Using velvetg - /usr/local/bin/velvetg | Version 1.2.10
[shovill] Using velveth - /usr/local/bin/velveth | Version 1.2.10
[shovill] Found spades version: 003014000
[shovill] Will use spades 003014000 options: --isolate and --merged
[shovill] Forced overwrite of existing --outdir ./
[shovill] Using tempdir: /tmp/OhjVKbgC5Z
[shovill] Changing into folder: /nfs/Genomics_DEV/projects/xdong/deve/pathogenseq/test
[shovill] Collecting raw read statistics with 'seqtk'
[shovill] Running: seqtk fqchk -q3 /nfs/Genomics_DEV/projects/xdong/deve/pathogenseq/test/SC18-6016-A.dehost.R1.fastq.gz >/tmp/apGBnAPsLG 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log
[shovill] Read stats: min_len = 52
[shovill] Read stats: avg_len = 281
[shovill] Read stats: max_len = 301
[shovill] Read stats: total_bp = 522426
[shovill] Estimating genome size by counting unqiue 21-mers > frequency 10
[shovill] Running: kmc -sm -m12 -t6 -k21 -ci10 /nfs/Genomics_DEV/projects/xdong/deve/pathogenseq/test/SC18-6016-A.dehost.R1.fastq.gz /tmp/TbxqcsWu1U/kmc /tmp/TbxqcsWu1U 2>&1 | sed 's/^/[kmc] /' | tee -a shovill.log
[kmc] **
Stage 1: 100%
Stage 2: 100%
[kmc]
[kmc] 1st stage: 0.888051s
[kmc] 2nd stage: 0.447705s
[kmc] 3rd stage: 0.002325s
[kmc] Total : 1.33808s
[kmc] Tmp size : 0MB
[kmc] Tmp size strict memory : 0MB
[kmc] Tmp total: 0MB
[kmc]
[kmc] Stats:
[kmc] No. of k-mers below min. threshold : 231887
[kmc] No. of k-mers above max. threshold : 0
[kmc] No. of unique k-mers : 231887
[kmc] No. of unique counted k-mers : 0
[kmc] Total no. of k-mers : 242653
[kmc] Total no. of reads : 928
[kmc] Total no. of super-k-mers : 35754
[shovill] Using genome size 0 bp
Illegal division by zero at /usr/local/bin/shovill line 162.