Segmentation fault on only one sample of multisample two pass mapping #1763
Description
Hello,
I'm trying to run STAR to do multisample two pass mapping and I'm launching jobs using snakemake. All of my samples (29/30 samples) run fine except one of them which reproducibly gives me a Segmentation fault (core dumped) error during the second pass of mapping on the mapping step. If I run this sample alone, it works fine and does not give an error. This sample is not the largest in the dataset (5.7G fast files vs highest are 8.4G) and so I think it is unlikely to be a RAM issue. Any ideas on how to fix this? Thanks!
The command I used was:
STAR --genomeDir /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/S
TAR_index --readFilesIn /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/01_fastp_trim/SR
R6843328_1.trimmed.fastq.gz /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/01_fastp_tri
m/SRR6843328_2.trimmed.fastq.gz --runThreadN 8 --readFilesCommand zcat --outTmpDir /local/scratch/ambenj/
slrmtmp.36192161/SRR6843328 --outFileNamePrefix /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_pre
process/02_STAR_align/pass2/SRR6843328. --sjdbFileChrStartEnd /labs/kingsley/ambenj/myosin/Metzger2018/an
alysis/RNA_preprocess/02_STAR_align/pass1/SRR6843319.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/
analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843320.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger201
8/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843321.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2
018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843322.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzge
r2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843323.SJ.out.tab /labs/kingsley/ambenj/myosin/Metz
ger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843324.SJ.out.tab /labs/kingsley/ambenj/myosin/Me
tzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843325.SJ.out.tab /labs/kingsley/ambenj/myosin/
Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843326.SJ.out.tab /labs/kingsley/ambenj/myosi
n/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843327.SJ.out.tab /labs/kingsley/ambenj/myo
sin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843328.SJ.out.tab /labs/kingsley/ambenj/m
yosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843329.SJ.out.tab /labs/kingsley/ambenj
/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843330.SJ.out.tab /labs/kingsley/ambe
nj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843331.SJ.out.tab /labs/kingsley/am
benj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843332.SJ.out.tab /labs/kingsley/
ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843333.SJ.out.tab /labs/kingsle
y/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843334.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843335.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843336.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843337.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843338.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843339.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843340.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843341.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843342.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843343.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843344.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843345.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843346.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843347.SJ.out.tab /labs/kingsley/ambenj/myosin/Metzger2018/analysis/RNA_preprocess/02_STAR_align/pass1/SRR6843348.SJ.out.tab --outFilterMatchNminOverLread 0.5 --outFilterScoreMinOverLread 0.5 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif
STAR log.out and slurm.out files provided: