[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, 16268058 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 16267725 kept reads (333 discarded)
[2018-07-14 20:37:02] Building transcriptome data files /scratch/6936770.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:37:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:46:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:07:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:27:50] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:27:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:55:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:07:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:19:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:32:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:43:17] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:49:20] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:53:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 23:23:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 23:36:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 23:47:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-15 00:00:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-15 00:12:44] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-15 00:21:14] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-15 00:25:54] Searching for junctions via segment mapping
[2018-07-15 12:32:20] Retrieving sequences for splices
[2018-07-15 12:34:15] Indexing splices
[2018-07-15 12:34:54] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 12:48:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 13:02:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 13:15:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 13:26:40] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 13:33:16] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 13:34:39] Joining segment hits
[2018-07-15 13:42:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 13:56:30] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 14:11:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 14:25:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 14:38:07] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 14:45:12] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 14:46:42] Joining segment hits
[2018-07-15 14:54:40] Reporting output tracks
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[2018-07-15 15:29:07] A summary of the alignment counts can be found in /scratch/6936770.1.linga/tophat2/align_summary.txt
[2018-07-15 15:29:07] Run complete: 19:07:53 elapsed