Question: Dealing with gff files in STAR
gravatar for valizad2
2.0 years ago by
United States/Urbana/University of Illinois at Urbana-Champaign
valizad20 wrote:

Hi all,

I am really having trouble doing the alignment in STAR using gff file. I tried downloading gtf files but I think finding and getting the files into cluster from Ensembl and USCS was very confusing. I was able to easily download gff files from NCBI but then using it in STAR is more complicated. I know I have to specify extra parameter for gff files and here is the code I am using:

STAR --runThreadN 12 --runMode genomeGenerate \
  --genomeDir /home/n-z/valizad2/Sepsis_RNAseq/HumanData/GenomeDirectory \
  --limitGenomeGenerateRAM 206609344554 \
  --genomeFastaFiles GCF_000001405.38_GRCh38.p12_genomic.fna \
  sjdbGTFtagExonParentTranscript Parent \
  --sjdbGTFfile GCF_000001405.38_GRCh38.p12_genomic.gff \
  --sjdbOverhang 100

Adding sjdbGTFtagExonParentTranscript Parent gives me the error below:

EXITING: FATAL INPUT ERROR: empty value for parameter "sjdbGTFtagExonParentTranscript Parent" in input "Command-Line-Initial"
SOLUTION: use non-empty value for this parameter

I don't know why it's telling me the parameter is empty. I would appreciate your help.


rna-seq • 1.8k views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 2.0 years ago by valizad20

Did you really run the command with sjdbGTFtagExonParentTranscript Parent, instead of --sjdbGTFtagExonParentTranscript Parent?

ADD REPLYlink written 2.0 years ago by h.mon31k

Yes, that was my mistake! Sorry. I ended up having to download the gtf files because I see in several places that using gff for gene counting is not a good idea.

Do you happen to know why I might have gotten this error when generating the index file using the gtf file?

Segmentation fault?

   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
ADD REPLYlink modified 2.0 years ago by h.mon31k • written 2.0 years ago by valizad20

Hi valizad2, please:

1) use the code button to format your post

2) do not post questions as answers, either open a new question, or post as a comment to my comment above, or edit your question.

I fixed for you this time.

ADD REPLYlink written 2.0 years ago by h.mon31k

Sure, Thanks! Sorry about that.

ADD REPLYlink written 2.0 years ago by valizad20

Try not to mention RAM allocation or check your space. I hope in this way. Thanks

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by k.kathirvel93260
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