[2019-07-17 19:14:32] Beginning TopHat run (v2.1.1)
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[2019-07-17 19:14:32] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 19:14:36] Checking for Bowtie index files (genome)..
[2019-07-17 19:14:36] Checking for reference FASTA file
[2019-07-17 19:14:36] Generating SAM header for Bowtie2Index/genome
[2019-07-17 19:14:43] Reading known junctions from GTF file
[2019-07-17 19:14:47] Preparing reads
	 left reads: min. length=150, max. length=150, 62071591 kept reads (5431 discarded)
	right reads: min. length=150, max. length=150, 62061678 kept reads (15344 discarded)
[2019-07-17 20:21:54] Building transcriptome data files /scratch/7775063.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 20:22:12] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 20:28:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 21:18:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 22:12:23] Resuming TopHat pipeline with unmapped reads
[2019-07-17 22:12:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 00:08:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 00:22:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 00:38:17] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 00:52:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 01:07:08] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 01:17:59] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 01:23:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 03:25:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 03:42:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 03:59:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 04:14:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 04:29:54] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 04:42:33] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 04:49:56] Searching for junctions via segment mapping
[2019-07-18 19:07:14] Retrieving sequences for splices
[2019-07-18 19:09:43] Indexing splices
[2019-07-18 19:10:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 19:23:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 19:36:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 19:48:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 20:02:35] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 20:11:21] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 20:13:53] Joining segment hits
[2019-07-18 20:38:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 20:52:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 21:06:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 21:20:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 21:32:38] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 21:41:24] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 21:43:34] Joining segment hits
[2019-07-18 22:07:34] Reporting output tracks
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[2019-07-19 00:26:47] A summary of the alignment counts can be found in /scratch/7775063.1.linga/tophat2/align_summary.txt
[2019-07-19 00:26:47] Run complete: 1 days 05:12:14 elapsed