STAR solo segmentation fault after 'started Solo counting'

Question

[bp22]

Dear all,

I have some 10x v3 single cell rna seq fastq files that I am trying to map to hg38 human genome using STAR aligner and generate read counts. However, I am getting the following error and hope that some of you can help:

zsh: segmentation fault  STAR --outSAMattributes All --outSAMtype BAM Unsorted --quantMode GeneCounts

I am using STAR version 2.7.10a and the STAR run fails after the following steps:

Nov 28 11:17:04 ..... started STAR run
Nov 28 11:17:06 ..... loading genome
Nov 28 11:20:17 ..... processing annotations GTF
Nov 28 11:20:35 ..... inserting junctions into the genome indices
Nov 28 11:21:30 ..... started mapping
Nov 28 12:19:41 ..... finished mapping
Nov 28 12:19:44 ..... started Solo counting
zsh: segmentation fault  STAR --outSAMattributes All --outSAMtype BAM Unsorted --quantMode GeneCounts

As per the generated log-file, the run fails after the following:

...
Nov 28 12:19:44 ..... started Solo counting
Nov 28 12:19:44 ... Starting Solo post-map for Gene
Nov 28 12:19:44 ... Finished allocating arrays for Solo 1.25473 GiB

Also, to start with I am running the following command:

STAR --outSAMattributes All \
     --outSAMtype BAM Unsorted \
     --quantMode GeneCounts \
     --readFilesCommand gunzip -c \
     --runThreadN 7 \
     --sjdbGTFfile $GTFFILE \
     --outReadsUnmapped Fastx \
     --outMultimapperOrder Random \
     --genomeDir $GENOMEDIR \
     --readFilesIn ${INPUTDIR}/R2.fastq.gz ${INPUTDIR}/R1.fastq.gz \
     --outFileNamePrefix $OUTPREFIX \
     --soloType CB_UMI_Simple \
     --soloCBwhitelist $WHITELIST \
     --soloUMIlen 12 \
     --soloCBlen 16 \
     --soloUMIstart 17 \
     --soloCBstart 1 \
     --soloBarcodeReadLength 0 \
     --soloUMIfiltering MultiGeneUMI_CR \
     --soloUMIdedup 1MM_CR \
     --clipAdapterType CellRanger4 \
     --outFilterScoreMin 30 \
     --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
     --soloCellFilter EmptyDrops_CR

Any help is appreciated.

Thank you

[ATpoint]

How much memory is available?

[bp22]

Hi ATpoint,

Thanks for your response. I am running it on a system with 64GB memory and 2TB of storage. I am allocating 7 out of 8 cores available and have ~ 1TB of free disk space. I have tried this alignment on the same system before on a different set of 10X scRNA-seq data and the run was successful. As you can see below:

...
Jul 15 15:03:14 ..... started Solo counting
Jul 15 15:03:14 ... Starting Solo post-map for Gene
Jul 15 15:03:14 ... Finished allocating arrays for Solo 2.07388 GiB
Jul 15 15:06:47 ... Finished reading reads from Solo files nCB=2853747, nReadPerCBmax=298352, yesWLmatch=0
Jul 15 15:09:26 ... Finished collapsing UMIs
Jul 15 15:09:26 ... Solo: writing raw matrix
Solo output directory directory created: RPE1_BRCA1_KO_TALA_RESSolo.out/Gene//raw/
Jul 15 15:09:41 ... Solo: cell filtering
cellFiltering: simple: nUMImax=81876; nUMImin=8188; nCellsSimple=5449
Jul 15 15:09:41 ... starting emptyDrops_CR filtering
Jul 15 15:09:42 ... finished ambient cells counting
Jul 15 15:09:42 ... finished SGT
Jul 15 15:09:42 ... finished ambient profile
Jul 15 15:09:42 ... candidate cells: minUMI=500; number of candidate cells=5234
Jul 15 15:09:42 ... finished observed logProb
Jul 15 15:09:48 ... finished simulations
Jul 15 15:09:49 ... finished emptyDrops_CR filtering: number of additional non-ambient cells=3799
Jul 15 15:09:57 ..... finished Solo counting
ALL DONE!

For this run I have also tried aligning just a part of the scRNA-seq data and it still failed at the same point. Hence, I am a bit puzzled by this segmentation fault and it might not be related to the avaiable memory for the run.

Best, BP

Answer 1

[bp22]

Dear all,

It seems like the issue was because of macOS update to macOS Ventura. A reinstall of STAR aligner solved the issue and now the run is sucessful on the same system.

Thank you.

Best, BP

[ATpoint]

+1 Thanks for following up!