stacks ref_map.pl ERROR 128

Question

[Ale]

Dear all, I'm trying to do the VARIANT CALLING starting from BAM files (alredy aligned to the reference genome) using STACKS and ref_map.pl function. The command is the following:

stacks ref_map -T 2 -o ./OUTPUT --popmap ./popmap_landrace.txt --samples ./BAM_files

and, as soon as it starts, this error apprears:

> Parsed population map: 140 files in 29 populations and 1 group. Found
> 140 sample file(s). Calling variants, genotypes and haplotypes...
> /usr/lib/stacks/bin/gstacks -I ./BAM_files/ -M ./popmap_landrace.txt
> -O ./OUTPUT -t 2 ref_map.pl: Aborted because the last command failed (128); see ref_map.log file. Last command executed by ref_map.pl was:
> /usr/lib/stacks/bin/gstacks -I ./BAM_files/ -M ./popmap_landrace.txt  -O ./OUTPUT -t 2

ref_map.log file is the following:

ref_map.pl version 2.60 started at 2023-04-26 12:02:10 /usr/lib/stacks/bin/ref_map.pl -T 2 -o ./OUTPUT --popmap ./popmap_landrace.txt --samples ./BAM_files

gstacks ========== /usr/lib/stacks/bin/gstacks -I ./BAM_files/ -M ./popmap_landrace.txt -O ./OUTPUT -t 2

gstacks: src/BamI.cc:104: void BamHeader::init_sdict(): Assertion `h_->sdict' failed.

ref_map.pl: Aborted because the last command failed (128). Last command executed by ref_map.pl was: /usr/lib/stacks/bin/gstacks -I ./BAM_files/ -M ./popmap_landrace.txt -O ./OUTPUT -t 2

I do not know where the error is, can someone help me?

[Pierre Lindenbaum]

check https://groups.google.com/g/stacks-users/c/r6END6-DxDs/m/ZKFLaLl1AwAJ

[Ale]

Thank you!