Error with indexing! STAR unable to access genome file SOS

Question

[j_eag]

I keep receiving the error:

EXITING because of INPUT ERROR: could not open genomeFastaFile: -

Does anyone know why this could be?

The code I run:

STAR \
  --runMode genomeGenerate \
  --genomeDir /scratch/e51/trial2/align/sequence/STARindex \
  --genomeFastaFiles /scratch/e51/trial2/align/sequence/genome/GRCm39.ens.fa \
  --runThreadN 12

I provide the full path, and I checked for permissions (the fasta file is -rw-rw-r--). I can't pinpoint what's wrong. Any help would be appreciated!

(Also I'm a somewhat beginner so forgive any errors in terminology)

[h.mon]

Is your original command split in multiple lines? Or is it just a single line? If it is a single line, you have to remove the back slashes (\).

[j_eag]

thanks so much! i should have known I was making a silly syntax mistake.

Would you by any chance know why i'm receiving a "killed" notification now? Could it be something in my line?

STAR --runMode genomeGenerate  --genomeDir /scratch/eag519/trial2/align/sequence/STARindex  --genomeFastaFiles /scratch/eag519/trial2/align/sequence/genome/GRCm39.ens.fa  --runThreadN 12
Oct 11 13:34:09 ..... started STAR run
Oct 11 13:34:09 ... starting to generate Genome files
Oct 11 13:34:56 ... starting to sort Suffix Array. This may take a long time...
Oct 11 13:35:06 ... sorting Suffix Array chunks and saving them to disk...
Killed

[jared.andrews07]

Probably out of memory. Monitor with top or such.

[j_eag]

I thought 50G would've been enough, interesting. Thanks, I'll try to add more, and also check out top.

Do you know if re-running the indexing command above will override the previous run's incomplete files?

[Ram]

Note: I cleaned this up as OP was just making a copy-paste mistake and the extra backslashes were irrelevant to the error they were facing.