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

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 • 632 views
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is there more than one entry for

grep NC_045512 combined_fasta.fa


?

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

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