[2019-07-03 17:15:17] Beginning TopHat run (v2.1.1)
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[2019-07-03 17:15:17] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 17:15:17] Checking for Bowtie index files (genome)..
[2019-07-03 17:15:17] Checking for reference FASTA file
[2019-07-03 17:15:17] Generating SAM header for Bowtie2Index/genome
[2019-07-03 17:15:19] Reading known junctions from GTF file
[2019-07-03 17:15:23] Preparing reads
	 left reads: min. length=150, max. length=150, 30999459 kept reads (420 discarded)
	right reads: min. length=150, max. length=150, 30999800 kept reads (79 discarded)
[2019-07-03 17:48:00] Building transcriptome data files /scratch/7505695.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 17:48:18] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 17:54:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:18:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:45:33] Resuming TopHat pipeline with unmapped reads
[2019-07-03 18:45:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 19:47:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 19:57:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:07:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:18:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:28:42] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:35:23] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 20:38:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 21:35:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 21:46:50] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 21:58:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:10:12] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 22:21:27] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 22:29:40] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 22:33:40] Searching for junctions via segment mapping
[2019-07-04 12:53:08] Retrieving sequences for splices
[2019-07-04 12:55:35] Indexing splices
[2019-07-04 12:57:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 13:12:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 13:26:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 13:39:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 13:52:48] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 14:01:08] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 14:02:54] Joining segment hits
[2019-07-04 14:26:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 14:41:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 14:56:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 15:10:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 15:24:31] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 15:32:59] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 15:34:55] Joining segment hits
[2019-07-04 15:57:18] Reporting output tracks
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[2019-07-04 17:26:49] A summary of the alignment counts can be found in /scratch/7505695.1.linga/tophat2/align_summary.txt
[2019-07-04 17:26:49] Run complete: 1 days 00:11:32 elapsed