CellRanger problem
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3 months ago

Hey, what's up?

I'm using the CellRanger for scRNA and this problem appears:

Generating STAR genome index (may take over 8 core hours for a 3Gb genome)...
Jun 07 19:02:11 ..... started STAR run
Jun 07 19:02:11 ... starting to generate Genome files
Jun 07 19:02:11 ... starting to sort Suffix Array. This may take a long time...
Jun 07 19:02:11 ... sorting Suffix Array chunks and saving them to disk...
Jun 07 19:02:18 ... loading chunks from disk, packing SA...
Jun 07 19:02:18 ... finished generating suffix array
Jun 07 19:02:18 ... generating Suffix Array index
Jun 07 19:02:19 ... completed Suffix Array index
Jun 07 19:02:19 ..... processing annotations GTF
Failed to make genome index with STAR.  This can occasionally be caused by setting the argument `memgb` too low.
Error was from running command '/dados/software/cellranger-7.1.0/lib/bin/STAR'
Command '['/dados/software/cellranger-7.1.0/lib/bin/STAR', '--runMode', 'genomeGenerate', '--genomeDir', '/dados1/1Olaf/CR/Viral_All/star', '--runThreadN', '1', '--genomeFastaFiles', '/dados1/1Olaf/CR/Viral_All/fasta/genome.fa', '--sjdbGTFfile', '/dados1/1Olaf/CR/Viral_All/genes/genes.gtf', '--limitGenomeGenerateRAM', '17179869184', '--genomeSAsparseD', '1', '--genomeSAindexNbases', '9', '--genomeChrBinNbits', '13']' died with <Signals.SIGSEGV: 11>.

Check stdout and stderr for more information.

What can I do to solve it?

RNA-seq STAR scRNA • 486 views
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What is the cellranger command you're using?

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And how much memory do you have assigned for this job? Likely you do not have enough memory for this process.

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I'm using cellranger mkref --genome=Viral --fasta=path.fna --genes=path.gtf

I have 126G RAM

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Try with atleast 32 GB of Memory rather than 16 GB specified by limitGenomeGenerateRAM option.

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