I am currently trying to build STAR index using the star aligner - for combined Human and SARS-Cov2 fasta files and GTF files. The command I am using is as follows :
STAR --runMode genomeGenerate --runThreadN 2 --limitGenomeGenerateRAM 174000000000 --genomeDir /my/output/directory/for_index_files --genomeFastaFiles combined_fasta.fa --sjdbGTFfile combined_gtf.gtf --sjdbOverhang 100
And using the respective fasta and GTF Files from ensembl.
I am however constantly running into the error : Duplicate entry "NC_045512.2" in sam header and samtools view: failed to add PG line to the header when submitting the star index files for further analysis (using seven bridges).
Kindly advise what could be the reason.