Hello everyone, I am using Ensembl-Vep tool with custom annotation feature for variant annotation. However, I got several warnings instead of the output

WARNING: Chromosome (locus id) not found in annotation sources or synonyms on line 2128

The locus id in the transcript file used and those in the gff file are different. I assume this is the issue.

A line from my gff file:

Chr1    phytozomev11    mRNA    2903    10817   .   +   .   ID=LOC_Os01g01010.1.MSUv7.0;Name=LOC_Os01g01010.1;pacid=33123311;longest=1;Parent=LOC_Os01g01010.MSUv7.0

My fasta file:

>ChrUn.fgenesh.mRNA.1 pacid=33098461 locus=ChrUn.fgenesh.gene.1 ID=ChrUn.fgenesh.mRNA.1.MSUv7.0 annot-version=v7.0 ATGGAGGTAGGAGGAACAGCCGGAGTCAATGTCGACGGCAGCCTCGTCGCCGGGTCAGGCAGCCGTTTTCATGGCCGCTGCACCAGTCGTCAAGGAGGAAGGAGCAGCGGGGAGGTGCTTCCTCACGGCATCGATGAGGGAGGACGCGAGGCACAGCTCTGCAATGGCAGGAGGTCAGCAGCCAGGAGGGAGGAGCAGGAGGCGTTTTTGCCACGTAGTGCTGGCACAGCACGCAGTGCGGTGGCTGCTGACAGCGAGGGCGCGCGTCGAGGCGGCCATGCGGTGAGGCGTGCGGTGGCTGCTCTCCTGCTTGCTGCGTGA

My vcf :

ChrUn.fgenesh.mRNA.10   677     .       C       T       68.0168 .       AB=0.264706;ABP=19.3602;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=3.25157;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=33.6667;MQMR=55.6;NS=1;NUMALT=1;ODDS=15.6615;PAIRED=1;PAIREDR=0.88;PAO=0;PQA=0;PQR=0;PRO=0;QA=333;QR=887;RO=25;RPL=5;RPP=3.25157;RPPR=3.79203;RPR=4;RUN=1;SAF=1;SAP=14.8328;SAR=8;SRF=11;SRP=3.79203;SRR=14;TYPE=snp      GT:DP:RO:QR:AO:QA:GL    0/1:34:25:887:9:333:-14.2898,0,-68.8824

Can anybody help me with creating a synonyms file? I dont understand what ID should I use.

Thanks in advance!