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

[Banthandor]

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 "=")

[dr-ashu-geno]

Hello,
May I ask how you solved this issue?
I am having the same error happening now..

Thank you in advance,