[2019-07-12 13:52:56] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:52:56] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:52:56] Checking for Bowtie index files (genome)..
[2019-07-12 13:52:56] Checking for reference FASTA file
[2019-07-12 13:52:56] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:52:58] Reading known junctions from GTF file
[2019-07-12 13:53:00] Preparing reads
	 left reads: min. length=151, max. length=151, 86231464 kept reads (5894 discarded)
	right reads: min. length=151, max. length=151, 86216436 kept reads (20922 discarded)
[2019-07-12 14:53:12] Building transcriptome data files /scratch/7678212.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:53:22] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 14:57:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:30:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 18:13:53] Resuming TopHat pipeline with unmapped reads
[2019-07-12 18:13:53] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 20:05:05] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 20:22:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 20:41:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 21:00:38] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 21:20:31] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 21:37:28] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 21:51:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 23:52:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 00:14:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 00:37:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 01:02:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 01:25:20] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 01:44:25] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 02:00:32] Searching for junctions via segment mapping
[2019-07-13 09:43:28] Retrieving sequences for splices
[2019-07-13 09:44:38] Indexing splices
[2019-07-13 09:45:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 09:56:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 10:07:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 10:19:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 10:31:48] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 10:42:01] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 10:48:37] Joining segment hits
[2019-07-13 11:08:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 11:21:20] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 11:35:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 11:49:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 12:02:39] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 12:12:44] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 12:18:35] Joining segment hits
[2019-07-13 12:40:41] Reporting output tracks
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[2019-07-13 13:57:25] A summary of the alignment counts can be found in /scratch/7678212.1.p8/tophat2/align_summary.txt
[2019-07-13 13:57:25] Run complete: 1 days 00:04:29 elapsed