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alexdobin / STAR

RNA-seq aligner
MIT License
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Genome indexing issue #899

Open primukh opened 4 years ago

primukh commented 4 years ago

Hi! I am trying to align my RNA-Seq reads to the human genome using STAR. I'm using the following syntax:

PBS -l nodes=3:ppn=4,vmem=80gb,walltime=03:00:00

STAR --runThreadN 12 --runMode genomeGenerate --genomeChrBinNbits 14 --genomeSAsparseD 2 --limitGenomeGenerateRAM 25000000000 --gen omeDir /N/slate/primukh/Hundley_Lab/Human_GRCh38/GRch38 --genomeFastaFiles GRCh38.p13.genome.fa --sjdbGTFfile gencode.v34.annotatio n.gtf

However, I keep getting the following error message: May 04 19:51:49 ..... inserting junctions into the genome indices /var/spool/torque/mom_priv/jobs/5194879.m2.SC: line 15: 16640 Killed STAR --runThreadN 12 --runMod e genomeGenerate --genomeChrBinNbits 14 --genomeSAsparseD 2 --limitGenomeGenerateRAM 25000000000 --genomeDir /N/sla te/primukh/Hundley_Lab/Human_GRCh38/GRch38 --genomeFastaFiles GRCh38.p13.genome.fa --sjdbGTFfile gencode.v34.annota tion.gtf

I don't know how to troubleshoot this error. Any help is really appreciated. Thanks.

alexdobin commented 4 years ago

Hi @primukh

please send me the Log.out file.

Cheers Alex