*** stack smashing detected ***: terminated

[christopher-vollmers]

Hi,

I am trying to use the STARsolo function to process full-length 10X cDNA reads. I parsed the data into read pairs (One containing the actual (~1200nt) read, the other the 10X cell barcode and UMI). The program (STARlong in this case) runs to completion when run with --outSAMtype SAM.

However, if I want to include SAMattributes CB and UB and am therefore required to --outSAMtype BAM SortedByCoordinate, the program always terminates in the BAM sorting stages. Command and error message are below. Any idea what could cause this?

Best, Chris

STARlong --genomeDir /home/ig88/refs/STARnew/lrgasp_grch38_sirvs/ --runThreadN 20 --readFilesIn fastqs/cellranger_input_S1_L001_R2_001.fastq fastqs/cellranger_input_S1_L001_R1_001.fastq --soloType Droplet --outFileNamePrefix StarTest --soloCBwhitelist ../737K-august-2016.txt --soloFeatures Gene GeneFull --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 2000 --scoreGapNoncan -20 --scoreGapGCAG -4 --scoreGapATAC -8 --scoreDelOpen -1 --scoreDelBase -1 --scoreInsOpen -1 --scoreInsBase -1 --alignEndsType Local --seedSearchStartLmax 50 --seedPerReadNmax 100000 --seedPerWindowNmax 1000 --alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000 --outSAMtype BAM SortedByCoordinate --outSAMattributes CR CY UR UY CB UB sM sS sQ NM

    STAR version: 2.7.10a   compiled: 2022-01-14T18:52:43-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source

Mar 13 15:19:49 ..... started STAR run Mar 13 15:19:50 ..... loading genome Mar 13 15:20:01 ..... started mapping Mar 13 15:49:24 ..... finished mapping Mar 13 15:49:26 ..... started Solo counting Mar 13 15:49:30 ..... finished Solo counting Mar 13 15:49:30 ..... started sorting BAM stack smashing detected : terminated Aborted (core dumped)

[alexdobin]

Hi Chris,

please try this patch: https://github.com/alexdobin/STAR/releases/tag/2.7.10a_alpha_220314 It fixed that was related to solo BAM sorting. If it does not help, please send a me a small subset of reads for testing.

Thanks! Alex

[christopher-vollmers]

HI Alex,

Thank you very much for getting back to me so quickly. I looked at the binary and source and it looks like it is missing the STARlong executable. Can I use the STAR executable these days to align reads up to 10kb long? Really appreciate your help. STAR could massively simplify how long read single cell experiments are analyzed these days.

Best, Chris

On Tue, Mar 15, 2022 at 6:40 AM Alexander Dobin @.***> wrote:

Hi Chris,

please try this patch: https://github.com/alexdobin/STAR/releases/tag/2.7.10a_alpha_220314 It fixed that was related to solo BAM sorting. If it does not help, please send a me a small subset of reads for testing.

Thanks! Alex

— Reply to this email directly, view it on GitHub https://github.com/alexdobin/STAR/issues/1508#issuecomment-1068001097, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGX7GL4IKUWXWL3WSFTMGBDVACHLZANCNFSM5QT7QFEA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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[christopher-vollmers]

Here are a few of the reads. These were parsed from a full-length cDNA long-read read experiment. I basically split up the single read spanning the whole cDNA molecule into two reads that look like a format cellranger or STAR might accept.

R2.subsampled.txt R1.subsampled.txt