[2019-04-23 20:56:54] Beginning TopHat run (v2.0.8)
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[2019-04-23 20:56:54] Checking for Bowtie
		  Bowtie version:	 0.12.9.0
[2019-04-23 20:56:54] Checking for Samtools
		Samtools version:	 0.1.19.0
[2019-04-23 20:56:54] Checking for Bowtie index files
[2019-04-23 20:56:54] Checking for Bowtie index files
[2019-04-23 20:56:54] Checking for reference FASTA file
[2019-04-23 20:56:54] Generating SAM header for /oak/stanford/groups/akundaje/marinovg/genomes/dm3/bowtie-indexes/dm3
	format:		 fastq
	quality scale:	 phred33 (default)
[2019-04-23 20:56:54] Reading known junctions from GTF file
[2019-04-23 20:56:55] Preparing reads
	 left reads: min. length=78, max. length=78, 18832203 kept reads (45838 discarded)
	right reads: min. length=78, max. length=78, 18838636 kept reads (39405 discarded)
[2019-04-23 21:06:31] Using pre-built transcriptome index..
[2019-04-23 21:06:33] Mapping left_kept_reads to transcriptome FlyBase with Bowtie 
[2019-04-23 21:17:23] Mapping right_kept_reads to transcriptome FlyBase with Bowtie 
[2019-04-23 21:27:51] Resuming TopHat pipeline with unmapped reads
[2019-04-23 21:27:52] Mapping left_kept_reads.m2g_um to genome dm3 with Bowtie 
[2019-04-23 21:31:03] Mapping left_kept_reads.m2g_um_seg1 to genome dm3 with Bowtie (1/3)
[2019-04-23 21:32:38] Mapping left_kept_reads.m2g_um_seg2 to genome dm3 with Bowtie (2/3)
[2019-04-23 21:34:14] Mapping left_kept_reads.m2g_um_seg3 to genome dm3 with Bowtie (3/3)
[2019-04-23 21:35:54] Mapping right_kept_reads.m2g_um to genome dm3 with Bowtie 
[2019-04-23 21:39:28] Mapping right_kept_reads.m2g_um_seg1 to genome dm3 with Bowtie (1/3)
[2019-04-23 21:41:18] Mapping right_kept_reads.m2g_um_seg2 to genome dm3 with Bowtie (2/3)
[2019-04-23 21:42:59] Mapping right_kept_reads.m2g_um_seg3 to genome dm3 with Bowtie (3/3)
[2019-04-23 21:44:44] Searching for junctions via segment mapping
[2019-04-23 21:46:58] Retrieving sequences for splices
[2019-04-23 21:47:03] Indexing splices
[2019-04-23 21:47:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/3)
[2019-04-23 21:47:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie (2/3)
[2019-04-23 21:48:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie (3/3)
[2019-04-23 21:48:35] Joining segment hits
[2019-04-23 22:14:22] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/3)
[2019-04-23 22:14:57] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie (2/3)
[2019-04-23 22:15:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie (3/3)
[2019-04-23 22:16:03] Joining segment hits
[2019-04-23 22:44:08] Reporting output tracks
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[2019-04-23 23:07:28] Run complete: 02:10:34 elapsed