what(): obsolete, invalid, or corrupt protobuf input

1. What were you trying to do?

Trying to call SVs

2. What did you want to happen?

get a .vcf with SVs

3. What actually happened?

filed to make a .pack file. 
  what():  obsolete, invalid, or corrupt protobuf input
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Stack trace path: /tmp/vg_crash_RUhGJb/stacktrace.txt

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

 /tmp/vg_crash_RUhGJb/stacktrace.txt

5. What data and command can the vg dev team use to make the problem happen?

vg construct -f -S -I insertions.fa -a -r N2_refrence.fna -v N2_2Formal_Manta.vcf > 6graph.vg vg convert 6graph.vg -a > 6graph.gbz vg index 6graph.vg -L -x 6graph.xg vg index -x 6graph.xg -g 6graph.gcsa -k 16 6graph.vg vg mpmap -x 6graph.xg -g 6graph.gcsa -f N2_2Formal_Combined.fq > 6graph.gam vg snarls 6graph.gbz > 6graph.snarls vg pack -x 6graph.gbz -g 6graph.gam -o 6graph.pack -Q 5


It terminated with the following error:
''
terminate called after throwing an instance of 'std::runtime_error'
  what():  obsolete, invalid, or corrupt protobuf input
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Stack trace path: /tmp/vg_crash_4OpdMA/stacktrace.txt

script used to create 'insertion.fa' file in construct command is following:
'''
def create_insertions_fa(vcf_file, output_file):
    with open(vcf_file, 'r') as vcf, open(output_file, 'w') as fa:
        for line in vcf:
            if line.startswith('#'):
                continue  # Skip header lines
            parts = line.strip().split('\t')
            #ralt = parts[4].rstrip('[') 
            #lalt = parts[4].lstrip(']')
            #if 'NC' in ralt
            ref, alt = parts[3], parts[4]
            if len(alt) > len(ref):  # Check if it's an insertion
                insertion_id = f"{parts[0]}_{parts[1]}"  # Using chromosome_position as ID
                sequence = alt
                fa.write(f">{insertion_id}\n{sequence}\n")

# Define the path for the input VCF file
vcf_file_path = '/home/rkapila/Short_read/Vgtoolkit/N2/Formal/N2_2Formal/Giraffee/N2_2Formal_Manta.vcf'

# Define the path for the output FASTA file in the same directory
output_file_path = '/home/rkapila/Short_read/Vgtoolkit/N2/Formal/N2_2Formal/Giraffee/insertions.fa'

# Call the function with the specified file paths
create_insertions_fa(vcf_file_path, output_file_path)

**6. What does running `vg version` say?**

vg version v1.44.0 "Solara" Compiled with g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 on Linux Linked against libstd++ 20210601 Built by anovak@octagon

vgteam / vg

what(): obsolete, invalid, or corrupt protobuf input #4251