Uninitialised readFeat is accessed and the programme terminates with a segment fault. - Githubissues

alexdobin / STAR

RNA-seq aligner

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Uninitialised readFeat is accessed and the programme terminates with a segment fault. #1530

Open iwakitakuma33 opened 2 years ago

iwakitakuma33 commented 2 years ago

Hello! Alex, Thanks for supporting STAR.

What I want to do. I want to map two reads to a index by running the following command The reads I am using are not reads created by single cell RNA-seq. STAR --genomeDir ... /... /STAR_mm10_index_default --readFilesIn ... /... /SRRxx/xxx1.fq ... /... /SRRxxx/xxx2.fq --outSAMtype BAM Unsorted
environment. mac book pro m1 chip
Phenomenon Execution result is segment fault.
What was done I debugged STAR using lldb. The readFeat initialisation process in lines 12 and 15 of SoloRead.cpp is not executed. Accessing an uninitialised readFeat at line 21 causes a segement fault.
Question. Is SoloRead executed when using reads created by single cell RNA-seq? Does a segement fault occur whenever soloType is None? Could there be missing options when running STAR?

Thanks very much.

alexdobin commented 2 years ago

Hi @iwakitakuma33

what version of STAR are you using? 2.7.10a had a bug which results in seg-faults sometimes. Instead, please use https://github.com/alexdobin/STAR/releases/tag/2.7.10a_alpha_220314