STAR: "Illegal instruction" error when using --clipAdapterType CellRanger4

Hello, I’m using STARsolo for aligning/demultiplexing BRB-seq libraries. These are bulk RNA-seq libraries with a very similar construct to 10x.

I recently saw the new option --clipAdapterType CellRanger4 which sounds super cool because that’s exactly the trimming we were doing. However, when using this option, after loading the genome, it exits with an “Illegal instruction” error:

Apr 23 17:24:05 ..... started STAR run
Apr 23 17:24:05 ..... loading genome
Apr 23 17:26:19 ..... started mapping
Illegal instruction

If I use all other options but this one, the run is successful. I tried removing some options, in case there would be some incompatibilities, but it kept failing. Here is the simplest command I’ve run

STAR \
--runMode alignReads \
--runThreadN 2 \
--soloStrand Forward \
--genomeDir ${starindex} \
--soloType CB_UMI_Simple \
--soloCBstart 1 \
--soloCBlen 12 \
--soloUMIstart 13 \
--soloUMIlen 9 \
--soloCellFilter None \
--soloCBwhitelist ${barcodefile} \
---clipAdapterType CellRanger4 \
--readFilesCommand zcat \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix bam/ \
--readFilesIn fastq/toto_R2.fastq.gz fastq/toto_R1.fastq.gz

Thanks in advance!

About this issue

  • Original URL
  • State: open
  • Created 3 years ago
  • Comments: 16 (4 by maintainers)

Most upvoted comments

You also may try only scheduling it to run on newer nodes, whether by targeting a specific set of nodes or limiting to a certain feature support in your scheduler. AVX2 has been present on all Intel Xeon processors since 2014, and all AMD Epyc processors since 2017, so only servers that are greater than 9 years old should encounter this problem.

If your nodes are virtualized I would speculate that some hypervisor configuration could break this as well, I’ve seen hypervisors not pass through all supported CPU flags into VMs but I’d expect the binary would still run because the support is actually there.

Hi @alexdobin - Will this issue get fixed so that users don’t need to recompile STAR to use --clipAdapterType CellRanger4? A lot of users use STAR as part of larger snakemake workflows for example, which rely on wrappers and automatic dependency install via conda/mamba.

Hey Alex,

Sorry for the delayed answer. I compiled my 2.7.8a release, and indeed it seems to work now.

Thanks for the tip!

Cheers