GeneFull_ExonOverIntron - Error of segmentation (core dumped) "${cmd}" "$@"

[wjbsb]

Hi,

I already used STAR for my single cell/nuclei and bulk RNA datasets.

So, I run a classical single cell/nuclei command line. But before the first mapping and after the loading a third threads, program stop with this error :` Error of segmentation (core dumped) "${cmd}" "$@"

I looked at my threads : I increase and decrease the number, always the same error.
I looked my limitBAMsortRAM : I increase and decrease the number, always the same error.
I built a new version of my index (human), always the same error.
I reduced the size of index, always the same error.
I checked fastq, classical data.
I changed the order of mates, always the same error. I tested different combinations...

So, after all that, I purge my system. I tested different versions of STAR (2.7.11b, 2.7.10a, 2.7.9a), always the same error.
I checked my nodes and others things in my system....from what I understand the problem is outside....

And on a whim, I remember a old technic when the bug is ...extremely unpleasant : test every parameters in my command.
So after few tests, I identified my error of segmentation :
When I used --soloFeatures GeneFull GeneFull_ExonOverIntron : there is error.
When I used --soloFeatures GeneFull : it's running.

I don't have any explication of that....

My STAR version installed in a conda environment separately.

This is my initial command:

STAR \
--genomeDir $genomeDir \
--readFilesType Fastx \
--readFilesIn $R2 $R1 \
--soloCellFilter  EmptyDrops_CR \
--soloCBwhitelist None \
--twopassMode Basic \
--outSAMtype BAM SortedByCoordinate \
--readFilesCommand zcat \
--runDirPerm All_RWX \
--outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM \
--soloType CB_UMI_Simple \
--soloCellReadStats Standard \
--soloFeatures GeneFull Velocyto GeneFull_ExonOverIntron \
--soloBarcodeReadLength 28 \
--limitBAMsortRAM 80000000000 \
--limitOutSJcollapsed 5000000 \
--limitSjdbInsertNsj 2212188 \
--runThreadN 12 \
--outFileNamePrefix $outFileNamePrefix