[2019-07-12 13:37:52] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:37:52] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:37:53] Checking for Bowtie index files (genome)..
[2019-07-12 13:37:53] Checking for reference FASTA file
[2019-07-12 13:37:53] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:37:54] Reading known junctions from GTF file
[2019-07-12 13:37:56] Preparing reads
	 left reads: min. length=151, max. length=151, 72360839 kept reads (142 discarded)
	right reads: min. length=151, max. length=151, 72353068 kept reads (7913 discarded)
[2019-07-12 14:28:11] Building transcriptome data files /scratch/7678208.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:28:20] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 14:32:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:22:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:13:04] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:13:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 17:45:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 18:00:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 18:16:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 18:33:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 18:49:14] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 19:01:26] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 19:11:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 20:49:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 21:06:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 21:23:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 21:42:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 21:58:34] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 22:11:50] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 22:24:00] Searching for junctions via segment mapping
[2019-07-12 23:12:48] Retrieving sequences for splices
[2019-07-12 23:13:58] Indexing splices
[2019-07-12 23:14:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-12 23:20:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-12 23:26:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-12 23:32:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-12 23:38:58] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-12 23:43:39] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-12 23:46:54] Joining segment hits
[2019-07-12 23:58:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 00:04:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 00:11:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 00:18:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 00:24:46] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 00:29:29] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 00:32:44] Joining segment hits
[2019-07-13 00:44:16] Reporting output tracks
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[2019-07-13 01:39:38] A summary of the alignment counts can be found in /scratch/7678208.1.p16/tophat2/align_summary.txt
[2019-07-13 01:39:38] Run complete: 12:01:45 elapsed