[2019-06-28 13:22:40] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:22:40] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:22:40] Checking for Bowtie index files (genome)..
[2019-06-28 13:22:40] Checking for reference FASTA file
[2019-06-28 13:22:40] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:22:46] Reading known junctions from GTF file
[2019-06-28 13:22:50] Preparing reads
	 left reads: min. length=150, max. length=150, 23160517 kept reads (386 discarded)
	right reads: min. length=150, max. length=150, 23160794 kept reads (109 discarded)
[2019-06-28 13:55:07] Building transcriptome data files /scratch/7287276.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:55:28] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:02:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:20:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:37:23] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:37:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:21:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:26:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:31:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:37:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 15:42:29] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 15:46:44] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 15:48:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:30:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 16:36:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 16:42:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:47:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:53:11] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:57:48] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:00:26] Searching for junctions via segment mapping
[2019-06-28 19:40:48] Retrieving sequences for splices
[2019-06-28 19:43:26] Indexing splices
[2019-06-28 19:44:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 19:47:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 19:50:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 19:53:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 19:56:31] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 19:58:43] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 19:59:30] Joining segment hits
[2019-06-28 20:07:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 20:10:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 20:13:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 20:17:03] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 20:20:06] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 20:22:26] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 20:23:17] Joining segment hits
[2019-06-28 20:31:46] Reporting output tracks
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[2019-06-28 21:13:44] A summary of the alignment counts can be found in /scratch/7287276.1.linga/tophat2/align_summary.txt
[2019-06-28 21:13:44] Run complete: 07:51:05 elapsed