no output at generating genome indexes

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larraitz larrañaga

Mar 16, 2023, 2:34:35 PMMar 16
to rna-star

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!!

Alexander Dobin

Mar 20, 2023, 3:33:34 PMMar 20
to rna-star
Hi Larraitz,

please specify full path to STAR executable. 

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