no output at generating genome indexes

[larraitz larrañaga]

Hi,

I am a beginner with STAR. I have to generate the genome indexes for an organism and I have to observe how increasing the number of threads decreases the execution time. 

I know that I have to use a fasta file and gtf file. However, i am not very sure which one do I have to dowload from ENSEMBL, because there many...

So i am running the following command: 
time ./STAR --runThreadN 2 

--runMode genomeGenerate --genomeDir /home/ulc/cursos/curso303/trabajo/outputTU --genomeFastaFiles /home/ulc/cursos/curso303/trabajo/GCF_000195955.2_ASM19595v2_genomic.fna 

--sjdbGTFfile /home/ulc/cursos/curso303/trabajo/GCF_000195955.2_ASM19595v2_genomic.gtf 

--genomeSAindexNbases 10 

--sjdbOverhang 100

It works, but it dos not give me any output, only the following file:

cat slurm-2340690.out

real    0m0.041s
user    0m0.001s
sys     0m0.001s

and a file Log.out empty.

what am I doing wrong?

Thank u!!

Larraitz

[Alexander Dobin]

Hi Larraitz,

please specify full path to STAR executable.