Thanks for the suggestion Kirill, but I think it has to do with the GTF file I'm using (actually I need to index the entire mm10 genome but only uploaded the chr19 GTF due to size).
In the log file everything seems to proceed fine until the the processing of the GTF file where I get an error for every GTF line. For example:
Sep 27 21:00:18 ..... Processing annotations GTF
WARNING: while processing sjdbGTFfile=/net/dulacfs2/dulacfs2/Users/dfernand/de/refdata/star.1.ucsc/chr19.gtf: no transcript_id for line:
chr19 mm10_knownGene exon 3066556 3066627 0 + . gene_id "uc033hid.1"; transcript_id "uc033hid.1"; gene_name "uc033hid.1";
WARNING: while processing sjdbGTFfile=/net/dulacfs2/dulacfs2/Users/dfernand/de/refdata/star.1.ucsc/chr19.gtf: no transcript_id for line:
chr19 mm10_knownGene exon 3576263 3576335 0 + . gene_id "uc033hif.1"; transcript_id "uc033hif.1"; gene_name "uc033hif.1";
This GTF was generated by UCSC but the same error also happens for genocde M6 GTF.