[2014-05-05 04:27:26] Beginning TopHat run (v2.0.8b)
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[2014-05-05 04:27:26] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 04:27:26] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 04:27:26] Checking for Bowtie index files
[2014-05-05 04:27:26] Checking for reference FASTA file
[2014-05-05 04:27:26] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 04:27:28] Preparing reads
	 left reads: min. length=60, max. length=101, 29933413 kept reads (9589 discarded)
[2014-05-05 04:39:38] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 05:19:03] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 05:22:15] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 05:25:50] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 05:29:38] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 05:33:33] Searching for junctions via segment mapping
[2014-05-05 05:55:10] Retrieving sequences for splices
[2014-05-05 05:57:07] Indexing splices
[2014-05-05 05:58:02] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 06:00:02] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 06:02:25] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 06:04:48] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 06:07:06] Joining segment hits
[2014-05-05 06:11:26] Reporting output tracks
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[2014-05-05 06:29:15] Run complete: 02:01:48 elapsed