Segmentation Fault error with STAR

Question

[valizad2]

Hi,

I am trying make the index file using STAR. I am getting segmentation fault error. Can anyone help me with that?

Thanks!

Oct 22 18:52:35 ..... started STAR run Oct 22 18:52:35 ... starting to generate Genome files Oct 22 18:53:44 ... starting to sort Suffix Array. This may take a long time... Oct 22 18:53:54 ... sorting Suffix Array chunks and saving them to disk... Oct 22 21:15:05 ... loading chunks from disk, packing SA... Oct 22 21:18:26 ... finished generating suffix array Oct 22 21:18:26 ... generating Suffix Array index Oct 22 21:21:13 ... completed Suffix Array index Oct 22 21:21:13 ..... processing annotations GTF /tmp/slurmd/job1091443/slurm_script: line 17: 3763135 Segmentation fault STAR --runThreadN 12 --runMode genomeGenerate --genomeDir /home/n-z/valizad2/Sepsis_RNAseq/HumanData/GenomeDirectory --limitGenomeGenerateRAM 206609344554 --genomeFastaFiles /home/n-z/valizad2/Sepsis_RNAseq/HumanData/Human_GeneGTF/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/n-z/valizad2/Sepsis_RNAseq/HumanData/Human_GeneGTF/Homo_sapiens.GRCh38.94.gtf --sjdbOverhang 100

[finswimmer]

Segmentation Faults are hard to debug. First think you should check is if you have enough space left on your device.

[valizad2]

Hi,

I am using a cluster so I imagine there should be enough space?

How much space would it need? To use STAR, we need to make a temporary directory in the scratch section in our cluster and that has 1TB of space.

[lieven.sterck]

No expert on Slurm cluster but did you request enough cores & memory for your job? CAn you get a resource usage report from this job?

Answer 1

[valizad2]

Hi Lieven.sterk,

I was able to resolve that issue with the help of biocluster support. so what happend was that I was requesting for 12 threads in my STAR code but the default for the cluster was one.