Dealing with gff files in STAR

Question

[valizad2]

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.

Thanks!

[h.mon]

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

[valizad2]

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

[h.mon]

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.

[valizad2]

Sure, Thanks! Sorry about that.

[k.kathirvel93]

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