--quantMode TranscriptomeSam segfaults

[roryk]

Hi Alex,

STAR 2.4.0e segfaults adding --quantMode TranscriptomeSAM:

/usr/local/bin/STAR --genomeDir /v-data/bcbio-nextgen/tests/data/genomes/mm9/star/ --readFilesIn /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz --runThreadN 1 --outFileNamePrefix /v-data/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591 --outReadsUnmapped Fastx --outFilterMultimapNmax 10 --outStd SAM --quantMode TranscriptomeSAM --outSAMunmapped Within --outSAMattributes NH HI NM MD AS --readFilesCommand zcat --outSAMattrRGline ID:1 PL:illumina PU:1_110907_ERP000591 SM:Test1 --outSAMstrandField intronMotif

Without TranscriptomeSAM it works fine.
Here is a gist of the log file:

https://gist.github.com/roryk/3aade4cc66af6db93496

[alexdobin]

Hi Rory,

I believed this is caused by the old genome - you would need to re-generate the genome with the latest version to use the --quantMode TranscriptomeSAM option. I have added a check for that in the latest patch: https://github.com/alexdobin/STAR/releases/tag/STAR_2.4.0f1

Cheers
Alex

[roryk]

Thanks a lot Alex, you are money.