Segmentation fault: 11 problem

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Yuande Tan

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Oct 13, 2016, 6:32:50 PM10/13/16

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Dear Alex,

I have 4-paired line RNA-seq data and want to map them to human reference genome using star 2.4.1 but I got Segmentation fault 11:

~/Documents$ bin/star --genomeDir ~/Documents/Homo_sapiens/UCSC/hg19/Sequence/StarIndex/ --runThreadN 4 --runMode alignReads --readFilesIn ~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17_L001_R1_001.fastq,~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17_L002_R1_001.fastq, ~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17_L003_R1_001.fastq,~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17_L004_R1_001.fastq ~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17_L001_R2_001.fastq,~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17_L002_R2_001.fastq, ~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17_L003_R2_001.fastq,~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17_L004_R2_001.fastq --sjdbGTFfile ~/Documents/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --outFileNamePrefix ~/Documents/Paul_data/Paul-32506491/19-39969519/2208L-10_S17 --limitIObufferSize 100000000 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 25000000000 --quantMode GeneCounts

Segmentation fault: 11

I ran successfuly one end-paired RNA-seq:

~/Documents$ bin/star --genomeDir ~/Documents/Homo_sapiens/UCSC/hg19/Sequence/StarIndex/ --runThreadN 1 --runMode alignReads --readFilesIn ~/Documents/Paul_data/Paul-32506491/18-39979437/2208L-1_S16_L004_R1_001.fastq ~/Documents/Paul_data/Paul-32506491/18-39979437/2208L-1_S16_L004_R2_001.fastq --sjdbGTFfile ~/Documents/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --outFileNamePrefix ~/Documents/Paul_data/Paul-32506491/18-39979437/2208L-1_S16_L004 --limitIObufferSize 100000000 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 25000000000 --quantMode GeneCounts

Oct 13 11:19:14 ..... Started STAR run

Oct 13 11:19:14 ..... Loading genome

Oct 13 11:23:42 ..... Processing annotations GTF

Oct 13 11:23:47 ..... Inserting junctions into the genome indices

Oct 13 11:25:45 ..... Started mapping

Oct 13 11:47:02 ..... Started sorting BAM

Oct 13 11:47:10 ..... Finished successfully

So Can I run multiple samples with star like above?

Would you like to tell me how to fix Segmentation fault: 11 problem?

Alexander Dobin

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Oct 18, 2016, 4:24:30 PM10/18/16

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Hi Yuande,

it should be:

--readFilesIn Sample1_R1,Sample2_R1,Sample3_R1 Sample1_R2,Sample2_R2,Sample3_R2

Note that R1 and R2 lists are separated by sapces, while samples in R1 and R2 lists are separated by commas (no spaces).

Also, please switch to a later release (2.5.x).

Cheers

Alex

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