Error: Segmentation fault (core dumped) during alignment to custom HBV genome

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huilei xu

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Oct 18, 2016, 8:54:49 AM10/18/16
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Hi Alex,

I created custom index for one HBV complete genome and then use regular command line to align the RNA-seq reads against it (expect small percentage of total reads belong to the virus). It never completes, only end up with "Segmentation fault (core dumped)". Any thoughts? The command line I use for creating index and alignment are as follows:

STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /indexes/ --genomeFastaFiles HBV.fa

STAR --runThreadN 22 --readFilesIn filein.fq --genomeDir indexes/HBV --outSAMunmapped Within --outFileNamePrefix STAR/HBV_output

Thanks.

Best,
Huilei

Alexander Dobin

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Oct 18, 2016, 5:03:12 PM10/18/16
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