I'm trying to run STAR alignment software on macOS Sierra to index the genome. The command is:
STAR --runThreadN 4 --runMode genomeGenerate --genomeFastaFiles $GENOME --sjdbGTFfile $ANOTATION --sjdbOverhang 99
And it gives the error:
Jun 28 15:21:51 ..... started STAR run Jun 28 15:21:51 ... starting to generate Genome files Genome_genomeGenerate.cpp:208:genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file ./GenomeDir//chrName.txt Solution: check that the path exists and you have write permission for this file
I have 'read and write' permissions for both input files. As suggested somewhere, I have tried to reduce the number of threads, and to increase the limit number of files that can be open at the same time with:
ulimit 10000000 ulimit -n
Nothing worked. Any ideas?