2015-06-05 09:13:34 - INFO: Disabling --hgvs; using --offline and no FASTA file found 2015-06-05 09:13:34 - Starting... 2015-06-05 09:13:34 - Read 2675 variants into buffer 2015-06-05 09:13:34 - Checking for existing variations ] [ 0% ] WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:6000001-7000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:6000001-7000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:6000001-7000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:6000001-7000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:6000001-7000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:6000001-7000000 WARNING: Could not find variation cache for Chromosome:3000001-4000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:6000001-7000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:2000001-3000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:5000001-6000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 WARNING: Could not find variation cache for Chromosome:1000001-2000000 WARNING: Could not find variation cache for Chromosome:1-1000000 WARNING: Could not find variation cache for Chromosome:4000001-5000000 2015-06-05 09:13:34 - Reading transcript data from cache and/or database 2015-06-05 09:13:35 - Retrieved 5678 transcripts (0 mem, 5678 cached, 0 DB, 0 duplicates) 2015-06-05 09:13:35 - Analyzing chromosome Chromosome 2015-06-05 09:13:35 - Caching custom annotations 2015-06-05 09:13:36 - Retrieved 1514 custom annotations (1514 pao1-genes) 2015-06-05 09:13:36 - Analyzing custom annotations 2015-06-05 09:14:12 - Processed 2675 total variants (70 vars/sec, 70 vars/sec total) 2015-06-05 09:14:12 - Wrote stats summary to TEST.txt_summary.html 2015-06-05 09:14:12 - See TEST.txt_warnings.txt for details of 132 warnings 2015-06-05 09:14:12 - Finished!