Generate Index Files for Both Human and SARS-Cov2 Reads : Error : samtools view: failed to add PG line to the header

Question

[universe_life]

Hi All,

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.

Thankyou.

[Pierre Lindenbaum]

is there more than one entry for

grep NC_045512 combined_fasta.fa

?

[universe_life]

Hi, I executed the command but only got one such entry for the same. It is in the header itself.

[GenoMax]

How is the command in your original post related to seven bridges? Are you using a VM in their environment or doing index generation on your end and then trying to use those files inc cloud environment at SevenB?

[universe_life]

Yes, I am doing index generation on my end and then using those files in the cloud environment at SevenB.