[2018-07-14 20:21:14] Beginning TopHat run (v2.1.1)
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[2018-07-14 20:21:14] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:21:15] Checking for Bowtie index files (genome)..
[2018-07-14 20:21:15] Checking for reference FASTA file
[2018-07-14 20:21:15] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:21:19] Reading known junctions from GTF file
[2018-07-14 20:21:23] Preparing reads
	 left reads: min. length=151, max. length=151, 17272729 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 17272413 kept reads (316 discarded)
[2018-07-14 20:42:39] Building transcriptome data files /scratch/6936767.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:42:56] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:50:44] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:09:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:27:53] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:27:53] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:56:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:05:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:15:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:26:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:36:45] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:43:28] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:48:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 23:23:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 23:34:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 23:44:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 23:53:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-15 00:03:06] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-15 00:09:36] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-15 00:14:42] Searching for junctions via segment mapping
[2018-07-15 10:27:29] Retrieving sequences for splices
[2018-07-15 10:29:50] Indexing splices
[2018-07-15 10:30:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 10:45:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 11:00:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 11:14:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 11:26:37] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 11:33:05] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 11:34:30] Joining segment hits
[2018-07-15 11:41:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 11:56:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 12:11:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 12:27:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 12:40:45] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 12:47:29] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 12:48:54] Joining segment hits
[2018-07-15 12:57:18] Reporting output tracks
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[2018-07-15 13:34:21] A summary of the alignment counts can be found in /scratch/6936767.1.linga/tophat2/align_summary.txt
[2018-07-15 13:34:21] Run complete: 17:13:06 elapsed