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

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.

star
• 2,255 views • link
written by universe_life • universe_life

is there more than one entry for

grep NC_045512 combined_fasta.fa

?

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by universe_life • universe_life

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?

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written by GenoMax GenoMax

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

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written by universe_life • universe_life

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