STUCK on building the Genome Index

66 views
Skip to first unread message

Aref

unread,
Oct 3, 2016, 11:33:36 AM10/3/16
to rna-star
Hello all, 

I am getting this error 
## here are the permissions
bash-4.1$ ls -ls
total 6384560
      3 drwxr-sr-x 3 ae112 ae112        138 Oct  2 18:30 fasta
     34 -rw-rw-r-- 1 ae112 ae112        539 Oct  2 22:07 genomeParameters.txt
      3 drwxr-sr-x 2 ae112 ae112         44 Oct  2 17:50 gtf
1971746 -rw-r--r-- 1 ae112 ae112 1408386097 Oct  2 18:08 Homo_sapiens.GRCh38.85.gtf
4412706 -rwxrwxrwx 1 ae112 ae112 3151425857 Oct  2 19:13 Homo_sapiens.GRCh38.dna.primary_assembly.fa
     66 -rw-rw-r-- 1 ae112 ae112      13380 Oct  2 22:07 Log.out
      3 drwx--S--- 2 ae112 ae112          0 Oct  2 22:07 _STARtmp

This is the command: 
bash-4.1$ STAR --runThreadN 8 --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles Homo_sapiens.GRCh38.dna.all.fa --sjdbGTFfile Homo_sapiens.GRCh38.85.gtf --sjdbOverhang 74
Oct 02 22:13:20 ..... started STAR run
Oct 02 22:13:21 ... starting to generate Genome files

EXITING because of INPUT ERROR: could not open genomeFastaFile: Homo_sapiens.GRCh38.dna.all.fa

Oct 02 22:13:21 ...... FATAL ERROR, exiting
bash-4.1$


Could you help me undrerstand what's going on? I am running an interactive session on the cluster STAR is loaded, I have 8 cores and ~40GB of memory reserved. 

Thank you very much. 

Yours, 
Aref 

Alexander Dobin

unread,
Oct 4, 2016, 1:26:50 PM10/4/16
to rna-star
Hi Aref,

the FASTA file in you directory is Homo_sapiens.GRCh38.dna.primary_assembly.fa (and the primary is the way to go), but your STAR command uses a different file

You need:
$ STAR --runThreadN 8 --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh38.85.gtf --sjdbOverhang 74

Cheers
Alex
Reply all
Reply to author
Forward
0 new messages