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
How much memory is available?
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:
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