[2019-07-12 13:39:05] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:39:05] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:39:06] Checking for Bowtie index files (genome)..
[2019-07-12 13:39:06] Checking for reference FASTA file
[2019-07-12 13:39:06] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:39:07] Reading known junctions from GTF file
[2019-07-12 13:39:09] Preparing reads
	 left reads: min. length=151, max. length=151, 71611595 kept reads (4844 discarded)
	right reads: min. length=151, max. length=151, 71599285 kept reads (17154 discarded)
[2019-07-12 14:30:40] Building transcriptome data files /scratch/7678211.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:30:49] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 14:35:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:33:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:39:36] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:39:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 18:22:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 18:37:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 18:53:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 19:10:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 19:27:05] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 19:41:11] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 19:53:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 21:42:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 22:00:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 22:19:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 22:38:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 22:57:16] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 23:12:59] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 23:27:06] Searching for junctions via segment mapping
[2019-07-13 00:20:56] Retrieving sequences for splices
[2019-07-13 00:22:10] Indexing splices
[2019-07-13 00:22:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 00:28:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 00:34:49] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 00:40:55] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 00:47:14] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 00:52:43] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 00:56:56] Joining segment hits
[2019-07-13 01:08:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 01:15:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 01:22:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 01:29:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 01:36:01] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 01:41:39] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 01:45:56] Joining segment hits
[2019-07-13 01:59:32] Reporting output tracks
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[2019-07-13 02:51:40] A summary of the alignment counts can be found in /scratch/7678211.1.c/tophat2/align_summary.txt
[2019-07-13 02:51:40] Run complete: 13:12:34 elapsed