segmentation fault when running with --soloType SmartSeq

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Assa Yeroslaviz

Mar 3, 2023, 6:41:01 AM3/3/23
to rna-star
I'm running STAR 2.7.10b with a scRNA-Seq from SMARTseq with the following command

STAR --runThreadN 20 --genomeDir $starIndex --sjdbGTFfile $gtf --sjdbOverhang 100 \
         --readFilesCommand zcat --readFilesIn $rawdata/$base.trimmed.R1.fastq.gz $rawdata/$base.trimmed.R1.fastq.gz \
         --soloType SmartSeq\
         --soloUMIdedup Exact --soloStrand Forward \
         --soloFeatures Gene GeneFull SJ \
         --outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM \
         --outFileNamePrefix $bamFiles/$base. --soloOutFileNames $base \
         --limitBAMsortRAM 168632718037 --readMapNumber 1000 \
         --outSAMtype BAM SortedByCoordinate

I have also increased the ulimit parameter to 5000, but I still get the error message when it starts mapping:

Mar 03 12:21:12 ..... started STAR run
Mar 03 12:21:13 ..... loading genome
Mar 03 12:25:04 ..... processing annotations GTF
Mar 03 12:25:26 ..... inserting junctions into the genome indices
Mar 03 12:27:25 ..... started mapping
Segmentation fault (core dumped)

I'm also attaching here the Log.out file in case you need it. But I can't find any errors in the log file

any ideas why it's crashing?




Alexander Dobin

Mar 3, 2023, 9:41:41 AM3/3/23
to rna-star
Hi Assa,

--soloType SmartSeq requires specifying cell IDs. It's easiest to do it in the --readFilesManifest file, which you use instead of --readFilesIn:
If you prefer to use --readFilesIn, then you need to specify cell IDs as read-groups in --outSAMattrRGline.


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