Monkey genome

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Z

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Jan 9, 2023, 10:26:41 AM1/9/23
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Hey Alex,

I am wondering if there is any caveat to using STAR for Cyno Monkey. I've managed to build a STAR index using Cyno fa and gtf. Then tried to align reads to it using STAR version: 2.7.10a using total memory of 60G and 16 cores in AWS pcluster. My code is as below:

    /home/reference/pipelines/current/bin/STAR --runThreadN 16 --genomeDir /home/reference/macFas6/STAR2710a151_RSEM131/star_rsem_ref/ --genomeLoad NoSharedMemory --readFilesIn LOLY005_fastp_R1.fastq.gz LOLY005_fastp_R2.fastq.gz --readFilesCommand zcat --peOverlapNbasesMin 10 --alignEndsType Local --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --limitBAMsortRAM 60000000000 --limitIObufferSize 200000000 500000000 --limitSjdbInsertNsj 1200000 --outFilterIntronMotifs None --outFilterMultimapNmax 50 --outSAMattributes All --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --outSAMunmapped Within --outFileNamePrefix LOLY005_ --quantMode TranscriptomeSAM GeneCounts --chimScoreMin 1 --chimSegmentMin 10 --chimOutType Junctions WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimOutJunctionFormat 1 --outFilterType BySJout --outSJfilterReads All --chimMultimapNmax 50

Then I received an error message as below. It seems like a memory issue. But I've been changing the setting in different ways to increase the memory but got no luck. I suspect there is something else going wrong. Could you please guide me further? Much appreciated.
 
source
Jan 06 16:05:33 ..... started STAR run
Jan 06 16:05:33 ..... loading genome

EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc
Possible cause 1: not enough RAM. Check if you have enough RAM 30262150041 bytes
Possible cause 2: not enough virtual memory allowed with ulimit. SOLUTION: run ulimit -v 30262150041

Jan 06 16:05:33 ...... FATAL ERROR, exiting


Thank you,

Alexander Dobin

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Jan 10, 2023, 9:27:37 AM1/10/23
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Hi Z,

it seems it could not allocate ~30GB.
Please try to increase it (before STAR run) with
ulimit -v 40000000

Cheers
Alex
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