ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf.

[melodyeeeee]

Hi, When I running this command : `vcf2maf=/data/jiaf/wes_cancer/biosoft/vcf2maf/vcf2maf.pl vep_path=~/miniconda3/envs/vep/bin/ GENOME=/data/jiaf/wes_cancer/biosoft/gsutil/gatk/hg19/v0/Homo_sapiens_assembly19.fasta vep_data=/data/jiaf/wes_cancer/data/vep/homo_sapiens/100_GRCh37

cat config | while read id do arr=(${id}) tumor=${arr[0]} perl ${vcf2maf} \ --input-vcf filter/clean/${tumor}.clean.vcf \ --output-maf annotation/vep/${tumor}_vep.maf \ --ref-fasta ${GENOME} \ --vep-path ${vep_path} \ --vep-data ${vep_data} \ --species homo_sapiens \ --ncbi-build GRCh37 \ 1>annotation/vep/${tumor}_vep.log 2>&1

done And here is the error that I'm getting: [W::fai_fetch] Reference chr10:101563814-101563816 not found in FASTA file, returning empty sequence Failed to fetch sequence in chr10:101563814-101563816 ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. I tried to search the solution to get rid of it, and based on the https://github.com/mskcc/vcf2maf/issues/257, I have changed the fasta file to "chr" format and still get this issue, is there any other solution? my fasta grep "chr10" Homo_sapiens_assembly19.fasta chr10 dna:chromosome chromosome:GRCh37:10:1:135534747:1`

Thank you!

[melodyeeeee]

I'm very sorry for the incorrect formatting, as this is the first time I've asked a question here, and would appreciate your understanding.

[chywang17]

Hi @melodyeeeee , I meet same problems. I wander know whether you have solved this issue.

[liuyang2006]

Dear developer,

I encountered exactly same error, even I change chr1 to 1, etc. Scripts:

perl vcf2maf.pl \
    --input-vcf ${in_vcf} --output-maf ${out_maf} \
    --vep-path /project/sli68423_1316/users/yang/conda/envs/vep/bin/vep\
    --vep-data /project/sli68423_1316/users/yang/.vep/ \
    --ref-fasta $ref

Below is error outputs:

[faidx] Failed to fetch sequence in :106293449-106293451
[W::fai_get_val] Reference :100903135-100903137 not found in FASTA file, returning empty sequence
[W::fai_get_val] Reference :100903135-100903137 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in :100903135-100903137
[W::fai_get_val] Reference :112824854-112824856 not found in FASTA file, returning empty sequence
[W::fai_get_val] Reference :112824854-112824856 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in :112824854-112824856
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 433.

[DayTimeMouse]

Hi @liuyang2006,

I have the same error, do you have any idea for this now?

Thanks in advance.