Hi,

I'm running STAR version=2.7.10a_alpha_220601 on some 10x 3' data.

STAR_2.7.10a --runThreadN 20 --soloType CB_UMI_Simple --soloUMIlen 12 --soloCellFilter EmptyDrops_CR --soloFeatures GeneFull --soloCBwhitelist ./3M-february-2018.txt --genomeDir /home/kath/storage2/dmel104_10a --outFilterType BySJout --alignIntronMax 100000 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 4715576210 --soloOutFileNames ZT00_10a_solo.out/ ZT00_features.tsv ZT00_barcodes.tsv ZT00_matrix.mtx --outFileNamePrefix ZT00_10a_ --readFilesCommand "zcat" --readFilesPrefix /home/kath/b1042/fatbody_sc_ZT/01.RawData/ZT0/ --readFilesIn ZT0_CKDL220015693-1A_H37TGDSX5_S1_L004_R2_001.fastq.gz ZT0_CKDL220015693-1A_H37TGDSX5_S1_L004_R1_001_trimmed.fastq.gz

The run makes it to

Jul 24 09:34:39 ..... started Solo counting
Jul 24 09:34:39 ... Starting Solo post-map for GeneFull
Jul 24 09:34:39 ... Finished allocating arrays for Solo 1.91906 GiB

and then segfaults. STAR version 2.7.9a is able to complete without error with the same run parameters.

Here's the output of gdb ~/bin/STAR_2.7.10a core.23748

Program terminated with signal 11, Segmentation fault.
#0 0x000000000046a1dc in SoloReadFeature::inputRecords(unsigned int**, unsigned int, std::vector<unsigned int, std::allocator >&, std::vector<readInfoStruct, std::allocator >&, SoloReadFlagClass&, std::vector<unsigned int, std::allocator >&, std::vector<unsigned int, std::allocator >&) ()
Missing separate debuginfos, use: debuginfo-install glibc-2.17-326.el7_9.x86_64 libgcc-4.8.5-44.el7.x86_64 libgomp-4.8.5-44.el7.x86_64 libstdc++-4.8.5-44.el7.x86_64 zlib-1.2.7-20.el7_9.x86_64

Going further with gdb than this is beyond my normal experience but I'm hoping it at least suggests possibilities.

Thanks,

• Bill