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Segmentation fault (core dumped) STAR #3

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MatosN opened this issue Dec 15, 2021 · 0 comments
Open

Segmentation fault (core dumped) STAR #3

MatosN opened this issue Dec 15, 2021 · 0 comments

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@MatosN
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MatosN commented Dec 15, 2021

Thanks for developing this pipeline.

I would like to test it with some of my samples in our computer (32C 128GbRam). After follow the installation steps I wasnt able to run the first job with STAR alignment, due to this error.
Any potential solution?
Many thanks

STAR --runThreadN 24 --genomeDir ./ref_files/v22
--outReadsUnmapped None
--chimSegmentMin 12
--chimJunctionOverhangMin 12
--chimOutJunctionFormat 1
--alignSJDBoverhangMin 10
--alignMatesGapMax 1000000
--alignIntronMax 1000000
--alignSJstitchMismatchNmax 5 -1 5 5
--outSAMstrandField intronMotif
--outSAMunmapped Within
--outSAMtype BAM Unsorted
--readFilesIn /home/biouser/RIMA/RIMA_pipeline/data/S174627_1.fastq.gz /home/biouser/RIMA/RIMA_pipeline/data/S174627_2.fastq.gz
--chimMultimapScoreRange 10
--chimMultimapNmax 10
--chimNonchimScoreDropMin 10
--peOverlapNbasesMin 12
--peOverlapMMp 0.1
--outSAMheaderHD @hd VN:1.4
--twopassMode Basic
--readFilesCommand zcat
--outFileNamePrefix analysis/star/S174627/S174627
--quantMode TranscriptomeSAM && mv analysis/star/S174627/S174627Aligned.out.bam analysis/star/S174627/S174627.unsorted.bam && samtools sort -T analysis/star/S174627/S174627TMP -o analysis/star/S174627/S174627.sorted.bam -@ 8 analysis/star/S174627/S174627.unsorted.bam && mv analysis/star/S174627/S174627Aligned.toTranscriptome.out.bam analysis/star/S174627/S174627.transcriptome.bam && mv analysis/star/S174627/S174627Chimeric.out.junction analysis/star/S174627/S174627.Chimeric.out.junction && mv analysis/star/S174627/S174627Log.final.out analysis/star/S174627/S174627.Log.final.out

Segmentation fault (core dumped)

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