Could not start STAR aligment due to fatal error : EXITING because of FATAL ERROR: could not create

[newton...@gmail.com]

Hi
   I wrote the shell like this way:
                /data/work/hanw/Star/STAR_2.3.0e/STAR  --runMode genomeGenerate --genomeDir /data/work/hanw/Star/GenomeDir --genomeFastaFiles /data/
reference/hg19 --runThreadN 8
           And then I nohup it to the working node , but every time the job EXITING itself immediately with showing the information below:
         
EXITING because of FATAL ERROR: could not create output file: ./Log.out
Check if the path ./ exists and you have permissions to write there

Mar 18 17:01:08 ...... FATAL ERROR, exiting

EXITING because of FATAL ERROR: could not create output file: ./Log.out
Check if the path ./ exists and you have permissions to write there

Mar 18 17:01:08 ...... FATAL ERROR, exiting
        What could be the reason for that ? someone could do me a favor?
        Thanks a lot

Regards

[Alexander Dobin]

Hi,

by default, STAR will write the output file in the current working directory, i.e. ./

You can change this path with --outFileNamePrefix option.

It looks like you do not have permissions to write in the directory from which you issued the nohup <YourScript>

Cheers

Alex

[Tomás Carrasco]

Nevermind I solved, I has to create the folder and then use that code, thanks

[Tomás Carrasco]

Hi to all, I'm dealing with the same problem, but 'm sure that I have permissions in he folder I do as follow:

claudio@venus[AT] sudo chmod -R 0777 .                                                                                        [ 9:53]

claudio@venus[AT] /Venus_Apple/programs/STAR/bin/STAR --runMode genomeGenerate --genomeDir star-AT --genomeFastaFiles /Venus_Apple/References_Genomes/AT/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --runThreadN 12

Nov 25 09:54:47 ..... started STAR run

Nov 25 09:54:47 ... starting to generate Genome files

genomeGenerate.cpp:150:genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file star-AT/genomeParameters.txt

Solution: check that the path exists and you have write permission for this file

Nov 25 09:54:47 ...... FATAL ERROR, exiting
claudio@venus[AT] sudo chmod -R 777 . 

And still the same error, please some help

El miércoles, 19 de marzo de 2014, 19:10:04 (UTC-3), Alexander Dobin escribió:

[Bart Van Der Hee]

I am receiving the same error. I am using Star 2.5.3a. I have tried adding RAM limits, thread limits, etc. The script has worked for me before, and I haven`t updated my computer since.
This is the script that previously worked:
/home/bart/RNA/STAR-2.5.3a/source/STAR --runThreadN 1 --runMode genomeGenerate --genomeDir /home/bart/RNA/Refgenome/Pig11Genome/STAR --genomeFastaFiles /home/bart/RNA/Refgenome/Pig11Genome/SscrofaENS11.fa --sjdbGTFfile /home/bart/RNA/Refgenome/Pig11Genome/SscrofaENS11.gtf --sjdbOverhang 99

And it gives me this error:
Aug 29 13:40:20 ..... started STAR run
Aug 29 13:40:20 ... starting to generate Genome files

genomeGenerate.cpp:167:genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file /home/bart/RNA/Refgenome/Pig11Genome/STAR/chrName.txt

Solution: check that the path exists and you have write permission for this file

Aug 29 13:40:51 ...... FATAL ERROR, exiting

I am running a 12 thread machine, with 64GB RAM.

Could someone help me?
Thanks in advance!




Op maandag 28 november 2016 18:11:05 UTC+1 schreef Tomás Carrasco:

[Alexander Dobin]

Hi Bart,

it looks like STAR cannot write into the /home/bart/RNA/Refgenome/Pig11Genome/STAR directory.

The /home/bart/RNA/Refgenome/Pig11Genome/STAR directory has to be created before the run and have rwx permissions - please check it.

Cheers

Alex

[Brett Vanderwerff]

Good fix this solves it for me too, all I had to do was make that directory and the error went away.

[dartvan...@gmail.com]

Hi there,

I had the same issue running as a root user (imagine my surprise when I didn't have the right permissions) and creating the folder solved it here too.

Why doesn't STAR check for the existence of the directory when provided with a directory name and attempt to create it with the permissions of the user, if it doesn't exist?

Cheers

Op dinsdag 29 augustus 2017 18:21:04 UTC+2 schreef Alexander Dobin:

[Alexander Dobin]

Hi @dartvanderleest

it seems like a relatively small inconvenience, but I will add it to my TODO list.

Cheers

Alex

[Dartolomeus van der Leest]

Thanks for the good and hard work! I really appreciate your tool either way.

Cheers

Op vr 25 jan. 2019 om 00:05 schreef Alexander Dobin <ado...@gmail.com>:

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