Immediate segmentation error when using STAR on SMART-Seq data
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23 months ago

I am trying to run STAR on Smart-seq 3 reads with the following command

STAR --runThreadN 8 --genomeDir /media/data/Reference_genomes/Drosophila_melanogaster/star/ --readFilesIn ./L1-scRNA-ism_S85_1.fastq ./L1-scRNA-ism_S85_2.fastq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ../../alignment/star-smart/L1-scRNA-ism/ --soloType SmartSeq --soloUMIdedup Exact --soloStrand Unstranded

My problem is that when running the command, I almost immediately get the following

May 27 10:19:03 ..... started STAR run
May 27 10:19:03 ..... loading genome
May 27 10:19:16 ..... started mapping
Segmentation fault (core dumped)

The fastqs are 1 GB each, from Drosophila, the reference genome is the "Release 6 plus ISO1 MT" version.

I have 12 threads and 62 GBs of RAM available, but increasing these parameters didn't seem to solve the problem. I found a similar issue in the STAR github repository, https://github.com/alexdobin/STAR/issues/966 but for an earlier version of STAR. I use 2.7.9a

segmentation smart-seq dumped scRNA-seq STAR • 298 views
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