Segmentation fault 11 encountered for STAR v2.7.10a

[yihming]

Hello,

I encountered a segmentation fault 11 error at the "sorting BAM" step when running 10x 5' data with STAR v2.7.10a within a Debian 10 docker container. The detailed Log.out.txt file is attached.

The detailed STAR command is below:

STAR --genomeDir genome_ref --runThreadN 28 --outFileNamePrefix result/ --soloType CB_UMI_Simple --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
     --soloUMIdedup 1MM_CR --outFilterScoreMin 30 --outSAMtype BAM SortedByCoordinate --outSAMattributes CR UR CY UY CB UB \
     --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 --soloBarcodeMate 1 --clip5pNbases 39 0 \
     --readFilesCommand zcat --readFilesIn \
     data/LIB5452773_SAM24411654_S1_L001_R1_001.fastq.gz,data/LIB5452773_SAM24411654_S1_L002_R1_001.fastq.gz \
     data/LIB5452773_SAM24411654_S1_L001_R2_001.fastq.gz,data/LIB5452773_SAM24411654_S1_L002_R2_001.fastq.gz \
     --soloCBwhitelist 737K-august-2016.txt --soloFeatures Gene GeneFull SJ Velocyto --soloCellFilter EmptyDrops_CR

However, when I ran exactly the same command with STAR v2.7.9a within a Debian 10 docker container, everything worked properly.

Could you please help me diagnose this issue?

In case you want to inspect the docker image we built, it's quay.io/cumulus/starsolo:2.7.10a, with Dockerfile specified here.

Thanks!

Sincerely,
Yiming

[Kekananen]

Yes this is definitely an issue on MacOS as well. Running:

STAR --runThreadN 8 --genomeDir resources/genomes/star/ --readFilesIn sample.R1.fastq.gz sample.R2.fastq.gz --readFilesCommand gunzip -c --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --outFileNamePrefix sample

Gives /bin/bash: line 2: 98204 Segmentation fault: 11. As you said Yiming, going back down to 9a fixed the problem.

[alexdobin]

Hi Yiming, Kathryn,

I cannot reproduce this error in my tests, using either set of parameters.
Does it happen if you limit the number of reads with (e.g. --readMapNumber 100000)?
Could you share a minimal subset of reads that still causes the error?

Thanks!
Alex

[Kekananen]

Sure, conveniently it's failing on the public test set we use. Though with the fresh install and regenerating the genome it's not the same segmentation error as before.

Running it again in a clean conda env with 2.7.10a on Monterey ver. 12.0.1:

STAR --runThreadN 8 --genomeDir ../resources/genomes/star/ --readFilesIn ../test/paired/10kReadsHiSeq/cancerPanel/rnaseq/SRR14136778_GSM5225207_SC623011_Homo_sapiens_sub_RNA-Seq_R1.fastq.gz ../test/paired/10kReadsHiSeq/cancerPanel/rnaseq/SRR14136778_GSM5225207_SC623011_Homo_sapiens_sub_RNA-Seq_R2.fastq.gz --readFilesCommand gunzip -c --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --outFileNamePrefix SRR14136778

resulting in:

        STAR version: 2.7.10a   compiled:  :/Users/travis/build/alexdobin/travis-tests/STARcompile/source
Feb 03 20:58:07 ..... started STAR run
Feb 03 20:58:07 ..... loading genome
Feb 03 20:58:50 ..... started mapping
[1]    22754 segmentation fault  STAR --runThreadN 8 --genomeDir ../resources/genomes/star/ --readFilesIn     

SRR14136778_GSM5225207_SC623011_Homo_sapiens_sub_RNA-Seq_R1.fastq.gz
SRR14136778_GSM5225207_SC623011_Homo_sapiens_sub_RNA-Seq_R2.fastq.gz

[yihming]

Hi Alex,

I attached --readMapNumber 100000 option to the command, but it seems also failed at the same step. Please check its log file Log2.out.txt.

Our data is internal, so I'll need to check with our collaborator to see if we could share a subset of the data with you.

Sincerely,
Yiming

[alexdobin]

Folks,

I think I fixed it: please try this patch:
https://github.com/alexdobin/STAR/releases/tag/2.7.10a_alpha_220207
The executables are not in the bin/ directories, but rather attached to the release.

Before the patch, Valgrind gave me an error on Kathryn's files, and after the patch, the error went away, so hopefully, it's fixed.

Cheers
Alex

[Kekananen]

It's working for me now on the test files as well. Thanks for fixing it so quickly.

[alexdobin]

Thanks for testing! I will make an official release in the next few days.