bcftools view could not parse the header / invalid contig name

[CaroZ655]

Hello,
I am trying call variants in a fungal genome. I have assembled the genome and merged my assembly to the existing assembly on Genebank (with Quikmerge).
I have then used Freebayes to generate the snps.vcf, then bgzipped the vcfs with Samtools, and then run Tabix.
When I try to run

module load BCFtools/1.21-GCC-13.3.0

while IFS= read -r i;
 do bcftools view -t ${SLURM_CPUS_PER_TASK} -i 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' /path/variants_filtering_annotation/${i}_snps_quickmerge.vcf.gz > /path/variants_filtering_annotation/${i}_quickmerge_filtered_snps.vcf.gz
done < "/path/M17_libs.txt"

I get in my .out file :

[E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<ID=NC_089422.1_Metarhizium_brunneum_chromosome_1,_complete_sequence,length=9557205>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<ID=NC_089423.1_Metarhizium_brunneum_chromosome_2,_complete_sequence,length=7414246>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<ID=NC_089428.1_Metarhizium_brunneum_chromosome_7,_complete_sequence,length=2793940>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<ID=NC_089427.1_Metarhizium_brunneum_chromosome_6,_complete_sequence,length=4124785>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<ID=NC_089425.1_Metarhizium_brunneum_chromosome_4,_complete_sequence,length=4578647>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<ID=NC_089424.1_Metarhizium_brunneum_chromosome_3,_complete_sequence,length=4701664>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<ID=NC_089426.1_Metarhizium_brunneum_chromosome_5,_complete_sequence,length=4217701>"
[W::bcf_hrec_check] Invalid contig name: "NC_089422.1_Metarhizium_brunneum_chromosome_1,_complete_sequence"
[W::bcf_hrec_check] Invalid contig name: "NC_089423.1_Metarhizium_brunneum_chromosome_2,_complete_sequence"
[W::bcf_hrec_check] Invalid contig name: "NC_089428.1_Metarhizium_brunneum_chromosome_7,_complete_sequence"
[W::bcf_hrec_check] Invalid contig name: "NC_089427.1_Metarhizium_brunneum_chromosome_6,_complete_sequence"
[W::bcf_hrec_check] Invalid contig name: "NC_089425.1_Metarhizium_brunneum_chromosome_4,_complete_sequence"
[W::bcf_hrec_check] Invalid contig name: "NC_089424.1_Metarhizium_brunneum_chromosome_3,_complete_sequence"
[W::bcf_hrec_check] Invalid contig name: "NC_089426.1_Metarhizium_brunneum_chromosome_5,_complete_sequence"

Is it something I have done wrong, or is it common ? Is there a way to work around this ?
Thank you !

[CaroZ655]

... Sorry I just realised there were comma in my headers, I removed them