Question: Segmentation Fault error with STAR
0
gravatar for valizad2
10 months ago by
valizad20
United States/Urbana/University of Illinois at Urbana-Champaign
valizad20 wrote:

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
rna-seq alignment • 536 views
ADD COMMENTlink written 10 months ago by valizad20

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

ADD REPLYlink written 10 months ago by finswimmer12k

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by valizad20

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?

ADD REPLYlink written 10 months ago by lieven.sterck5.5k
0
gravatar for valizad2
10 months ago by
valizad20
United States/Urbana/University of Illinois at Urbana-Champaign
valizad20 wrote:

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.

ADD COMMENTlink written 10 months ago by valizad20
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