[2019-07-13 00:08:06] Beginning TopHat run (v2.1.1)
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[2019-07-13 00:08:06] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-13 00:08:06] Checking for Bowtie index files (genome)..
[2019-07-13 00:08:06] Checking for reference FASTA file
[2019-07-13 00:08:06] Generating SAM header for Bowtie2Index/genome
[2019-07-13 00:08:08] Reading known junctions from GTF file
[2019-07-13 00:08:09] Preparing reads
	 left reads: min. length=150, max. length=150, 64818606 kept reads (5780 discarded)
	right reads: min. length=150, max. length=150, 64808291 kept reads (16095 discarded)
[2019-07-13 00:47:49] Building transcriptome data files /scratch/7682058.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-07-13 00:47:59] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-13 00:52:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-13 01:25:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-13 02:01:17] Resuming TopHat pipeline with unmapped reads
[2019-07-13 02:01:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 02:46:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 02:53:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 03:01:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 03:08:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 03:15:32] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 03:21:11] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 03:24:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 04:12:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 04:19:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 04:27:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 04:35:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 04:42:47] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 04:48:46] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 04:52:53] Searching for junctions via segment mapping
[2019-07-13 10:19:18] Retrieving sequences for splices
[2019-07-13 10:20:29] Indexing splices
[2019-07-13 10:21:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 10:26:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 10:31:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 10:37:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 10:42:26] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 10:46:23] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 10:47:58] Joining segment hits
[2019-07-13 10:56:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 11:02:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 11:07:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 11:13:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 11:18:50] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 11:22:44] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 11:24:14] Joining segment hits
[2019-07-13 11:33:17] Reporting output tracks
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[2019-07-13 12:35:47] A summary of the alignment counts can be found in /scratch/7682058.1.p/tophat2/align_summary.txt
[2019-07-13 12:35:47] Run complete: 12:27:41 elapsed