Thank you, it worked.
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Redirecting the Log.txt file from a STAR indexing run
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
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GenoMax
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1 answer
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.
Thank you, it worked.
so, flag this question as answered please (green flag on the left)
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Pierre Lindenbaum
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