Redirecting the Log.txt file from a STAR indexing run

Question

[biomagician]

When I run this command to index a genome with STAR:

STAR --runMode genomeGenerate --genomeDir output/genome/ecoli/index --genomeFastaFiles output/genome/ecoli/sequence/ecoli.fa --sjdbGTFfile output/genome/ecoli/annotation/ecoli.gtf > output/genome/ecoli/index/message.txt

a Log.txt file is created in my working directory with details about the indexation of the genome. Does anybody know how to write the Log.txt in another directory? Thanks. Cristian

Answer 1

[GenoMax]

From STAR manual

STAR produces multiple output files. All files have standard name, however, you can change the file prefixes using --outFileNamePrefix /path/to/output/dir/prefix. By default, this parameter is ./, i.e. all output files are written in the current directory.

This would write all output files to the directory you specify.

If you only need to redirect stderr/stdout (as indicated in your command) then take a look at this.

[biomagician]

Thank you, it worked.

[Pierre Lindenbaum]

Thank you, it worked.

so, flag this question as answered please (green flag on the left)