Segmentation fault on only one sample of multisample two pass mapping

[ambenj]

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:

SRR6843328.Log.out.txt
slurm-36192161.out.txt

[alexdobin]

Hi Alyssa,

this could be a bug, could you please send me the SJ.out.tab files, as well as the trimmed SRR6843328_* files.
I will try to reproduce and fix it.

[ambenj]

Hi Alex,

Thanks for looking into this. Here is a gdrive link to a tar.gz folder with the SJ.out.tab files, the trimmed SRR6843328_* files and the index in case you need that too. Let me know if this method of sharing the files doesn't work or you prefer something else.

https://drive.google.com/drive/folders/1ScsIbWy_KGoN_JQTBWPUt5Cnt2LIhfFz?usp=sharing

[alexdobin]

Hi Alyssa,

I think I have fixed the bug; please try out this patch:
https://github.com/alexdobin/STAR/releases/tag/STAR_2.7.10b_alpha_230301

Many thanks for reporting this bug and the test files!

[ambenj]

Awesome thanks! I will test this out and report back.

[ambenj]

Hi Alex,

The patch worked! Thanks so much for your help!