[2019-07-05 11:19:08] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:19:08] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:19:08] Checking for Bowtie index files (genome)..
[2019-07-05 11:19:08] Checking for reference FASTA file
[2019-07-05 11:19:08] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:19:13] Reading known junctions from GTF file
[2019-07-05 11:19:16] Preparing reads
	 left reads: min. length=150, max. length=150, 21799726 kept reads (1666 discarded)
	right reads: min. length=150, max. length=150, 21786591 kept reads (14801 discarded)
[2019-07-05 11:44:07] Building transcriptome data files /scratch/7534477.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:44:25] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:50:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:09:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:31:05] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:31:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:48:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:50:13] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:51:34] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:53:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:54:31] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:55:58] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:57:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:18:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:20:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:22:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:24:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:26:45] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:28:46] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:30:35] Searching for junctions via segment mapping
[2019-07-05 14:56:26] Retrieving sequences for splices
[2019-07-05 14:59:08] Indexing splices
[2019-07-05 15:00:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:01:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:02:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:03:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:04:29] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:05:31] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:06:23] Joining segment hits
[2019-07-05 15:11:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:13:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:14:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:16:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:17:45] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:19:09] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:20:23] Joining segment hits
[2019-07-05 15:26:42] Reporting output tracks
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[2019-07-05 16:33:17] A summary of the alignment counts can be found in /scratch/7534477.1.linga/tophat2/align_summary.txt
[2019-07-05 16:33:17] Run complete: 05:14:08 elapsed