EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "–-runThreadN" in input "Command-Line-Initia

[Wei Guo]

Hi guys,

I tried to use STAR as shown as below:

STAR –-runThreadN 4 —-runMode genomeGenerate —-genomeDir /lfs/scratch/weiguo/pra_airway/SIRFILES/genomeDir —genomeFastaFiles /lfs/scratch/weiguo/pra_airway/SIRFILES/ENSEMBL.homo_sapiens.release_75/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa —-sjdbGTFfile /lfs/scratch/weiguo/pra_airway/SIRFILES/ENSEMBL.homo_sapiens.release_75/Homo_sapiens.GRCh37.75.gtf

But errors happened:

EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "–-runThreadN" in input "Command-Line-Initial"

SOLUTION: use correct parameter name (check the manual)

What will I do?  THANKS

WEI 

[Alexander Dobin]

Hi Wei,

it seems to me you have strange characters instead of dashes --, please check that.

If it still does not work, please send me your Log.out file.

Cheers

Alex

[Wei Guo]

Hi Alex,

I did it again as below:

STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /genomeDir --genomeFastaFiles Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh37.75.gtf 

"EXITING because of FATAL INPUT PARAMETER ERROR: for generating genome with annotations (--sjdbFileChrStartEnd or --sjdbGTFfile options)

you need to specify non-zero --sjdbOverhang

SOLUTION: re-run genome generation specifying non-zero --sjdbOverhang, which ideally should be equal to OneMateLength-1, or could be chosen generically as ~100"

Please find the Log.out file attached.

Thanks so much.

Wei 

Feb 13 10:42:50 ..... Started STAR run

[Wei Guo]

On Thursday, February 12, 2015 at 11:35:48 PM UTC-5, Alexander Dobin wrote:

[Alexander Dobin]

Hi Wei,

you need to add another parameter --sjdbOverhang <N> when generating genome with annotations, which could be simply 100, or, ideally = readLength-1.

Cheers

Alex

[Wei Guo]

Hi Alex,

I did it again as below:

STAR --sjdbOverhang 50 --runThreadN 4 --runMode genomeGenerate --genomeDir /genomeDir --genomeFastaFiles Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh37.75.gtf 

"EXITING because of FATAL ERROR: could not create output file /genomeDir/genomeParameters.txt

Solution: check that the genomeDir directory exists and you have write permission for it: genomeDir=/genomeDir"

Please find the Log.out file attached.

Thanks

Wei 

[Alexander Dobin]

Hi Wei,

you need to create the genome directory before you run STAR. In you case, you need to do 

$mkdir /genomeDir

However, I am not sure if you really want to create the directory in the root directory /, and you may not have permission to do so. It's best to create this directory somewhere within your home directory.

Cheers

Alex