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SamahElmahdi / Glaucoma-variant-calling

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Encountered internal HISAT2 exception (#1) and reference slected chromosomes (3,6,11,20) #11

Open fayrouzAli opened 4 years ago

fayrouzAli commented 4 years ago

Encountered internal HISAT2 exception (#1) search on biostar .... Make sure you have enough room on the hard drive for HISAT2 to write temporary files while building an index. Despite Eng. Mohamed have increased the VM space I have to delete all old files and trying again

fayrouzAli commented 4 years ago

Still don't work after I deleted the old files.... the same error Hisat2 manual If you use --snp, --ss, and/or --exon, hisat2-build will need about 200GB RAM for the human genome size as index building involves a graph construction. Otherwise, you will be able to build an index on your desktop with 8GB RAM. fayrouz

fayrouzAli commented 4 years ago

we decided to choose a fewer number of chromosomes according to literature that mentioned that chromosomes 3,6,11,22 have a mutations for PCAG. using this link too download Index of ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/

chromosome 3 ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.3.fa.gz

chromosome 6 ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.6.fa.gz

chromosome 11 ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.11.fa.gz

chromosome 20 ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz