[2014-05-27 21:01:57] Beginning TopHat run (v2.0.8b)
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[2014-05-27 21:01:57] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 21:01:57] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 21:01:57] Checking for Bowtie index files
[2014-05-27 21:01:57] Checking for reference FASTA file
[2014-05-27 21:01:57] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 21:02:00] Preparing reads
	 left reads: min. length=60, max. length=101, 27916411 kept reads (1485 discarded)
[2014-05-27 21:14:09] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 21:59:07] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 22:03:16] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 22:07:38] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 22:11:51] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 22:15:52] Searching for junctions via segment mapping
[2014-05-27 22:22:30] Retrieving sequences for splices
[2014-05-27 22:24:34] Indexing splices
[2014-05-27 22:25:11] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 22:29:49] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 22:34:57] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 22:39:52] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 22:45:15] Joining segment hits
[2014-05-27 22:51:27] Reporting output tracks
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[2014-05-27 23:09:03] Run complete: 02:07:05 elapsed