[2018-07-14 20:20:53] Beginning TopHat run (v2.1.1)
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[2018-07-14 20:20:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:20:53] Checking for Bowtie index files (genome)..
[2018-07-14 20:20:53] Checking for reference FASTA file
[2018-07-14 20:20:53] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:20:56] Reading known junctions from GTF file
[2018-07-14 20:21:01] Preparing reads
	 left reads: min. length=151, max. length=151, 15116474 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 15116171 kept reads (303 discarded)
[2018-07-14 20:35:09] Building transcriptome data files /scratch/6936769.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:35:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:43:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 20:59:48] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:16:32] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:16:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:39:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 21:49:39] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:00:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:10:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:19:27] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:24:55] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:29:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:56:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 23:06:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 23:17:16] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 23:27:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 23:37:44] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 23:44:22] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:48:29] Searching for junctions via segment mapping
[2018-07-15 09:10:35] Retrieving sequences for splices
[2018-07-15 09:12:35] Indexing splices
[2018-07-15 09:13:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 09:23:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 09:34:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 09:45:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 09:55:01] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 10:00:52] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 10:02:15] Joining segment hits
[2018-07-15 10:09:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 10:20:55] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 10:33:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 10:44:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 10:53:45] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 10:59:36] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 11:00:54] Joining segment hits
[2018-07-15 11:08:10] Reporting output tracks
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[2018-07-15 11:40:38] A summary of the alignment counts can be found in /scratch/6936769.1.linga/tophat2/align_summary.txt
[2018-07-15 11:40:38] Run complete: 15:19:45 elapsed