chromosome_scaffolder.sh: AUTO_REP_COV_THRESH=: syntax error: operand expected (error token is "=")

I'm getting the following error:

/apps/gent/RHEL8/zen2-ib/software/MaSuRCA/4.1.0-GCC-11.3.0/bin/chromosome_scaffolder.sh: line 227: let: AUTO_REP_COV_THRESH=: syntax error: operand expected (error token is "=")

I used the following command:

chromosome_scaffolder.sh -r reference.fna -q query.fa -t 32 -i 95 -v -s longreads.fastq

Many thanks for making this software available.

This is the complete log file:

shift
[[ 2 > 0 ]]
key=-s
case $key in
READS=20929_S64018_PL100266327-1_A01.ccs.fastq
shift
shift
[[ 0 > 0 ]] ++ basename GCF_023373825.1_ASM2337382v1_genomic.fna
REF_CHR=GCF_023373825.1_ASM2337382v1_genomic.fna ++ basename filtered.asm.cns.fa
HYB_CTG=filtered.asm.cns.fa.split
HYB_POS=filtered.asm.cns.fa.split.posmap
PREFIX=GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split
'[' '!' -s GCF_023373825.1_ASM2337382v1_genomic.fna ']'
'[' '!' -s GCF_023373825.1_ASM2337382v1_genomic.fna ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.gaps.success ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.split.success ']'
'[' 1 -gt 0 ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.noise.success ']'
'[' 0 -lt 1 ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.readalign.success ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.coverage.success ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.align1.success ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.filter1.success ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.merge1.success ']'
'[' '!' -e GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.break.success ']'
log 'Splitting query contigs at suspect locations' ++ date
dddd='Tue Mar 21 16:28:50 CET 2023'
echo -e '[Tue Mar 21 16:28:50 CET 2023] Splitting query contigs at suspect locations'
rm -f GCF_023373825.1_ASM2337382v1_genomic.fna.filtered.asm.cns.fa.split.align2.success ++ awk '{print $4}' filtered.asm.cns.fa.split.posmap.coverage ++ sort -n -S 10% ++ uniq -c ++ head -n 1 ++ awk '{print int($2/.8)}' ++ sort -nrk1,1 -S 10%
let AUTO_REP_COV_THRESH= /apps/gent/RHEL8/zen2-ib/software/MaSuRCA/4.1.0-GCC-11.3.0/bin/chromosome_scaffolder.sh: line 227: let: AUTO_REP_COV_THRESH=: syntax error: operand expected (error token is "=")

alekseyzimin / masurca

chromosome_scaffolder.sh: AUTO_REP_COV_THRESH=: syntax error: operand expected (error token is "=") #316