[2019-07-03 18:37:53] Beginning TopHat run (v2.1.1)
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[2019-07-03 18:37:53] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 18:37:53] Checking for Bowtie index files (genome)..
[2019-07-03 18:37:53] Checking for reference FASTA file
[2019-07-03 18:37:53] Generating SAM header for Bowtie2Index/genome
[2019-07-03 18:37:56] Reading known junctions from GTF file
[2019-07-03 18:37:58] Preparing reads
	 left reads: min. length=150, max. length=150, 28443865 kept reads (387 discarded)
	right reads: min. length=150, max. length=150, 28444175 kept reads (77 discarded)
[2019-07-03 18:55:38] Building transcriptome data files /scratch/7505707.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 18:55:48] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 19:00:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:13:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:26:23] Resuming TopHat pipeline with unmapped reads
[2019-07-03 19:26:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 19:53:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 19:57:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:02:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:06:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:11:03] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:14:27] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 20:16:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 20:44:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:49:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:54:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:58:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 21:03:43] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 21:07:34] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 21:09:56] Searching for junctions via segment mapping
[2019-07-03 22:29:01] Retrieving sequences for splices
[2019-07-03 22:30:12] Indexing splices
[2019-07-03 22:30:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-03 22:32:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-03 22:34:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-03 22:37:04] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-03 22:39:12] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-03 22:40:38] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-03 22:41:22] Joining segment hits
[2019-07-03 22:45:52] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-03 22:48:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-03 22:50:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-03 22:52:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-03 22:54:46] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-03 22:56:12] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-03 22:56:59] Joining segment hits
[2019-07-03 23:01:35] Reporting output tracks
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[2019-07-03 23:24:31] A summary of the alignment counts can be found in /scratch/7505707.1.p8/tophat2/align_summary.txt
[2019-07-03 23:24:31] Run complete: 04:46:38 elapsed