[2019-07-05 11:11:51] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:11:51] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:11:51] Checking for Bowtie index files (genome)..
[2019-07-05 11:11:51] Checking for reference FASTA file
[2019-07-05 11:11:51] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:11:56] Reading known junctions from GTF file
[2019-07-05 11:11:59] Preparing reads
	 left reads: min. length=150, max. length=150, 22892285 kept reads (1822 discarded)
	right reads: min. length=150, max. length=150, 22878387 kept reads (15720 discarded)
[2019-07-05 11:39:44] Building transcriptome data files /scratch/7534484.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:40:01] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:46:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:10:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:35:56] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:35:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:49:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:50:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:52:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:53:36] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:55:01] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:56:25] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:57:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:16:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:19:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:22:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:24:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:27:18] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:29:45] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:32:11] Searching for junctions via segment mapping
[2019-07-05 15:37:44] Retrieving sequences for splices
[2019-07-05 15:40:00] Indexing splices
[2019-07-05 15:41:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:42:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:44:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:45:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:46:24] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:47:35] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:48:37] Joining segment hits
[2019-07-05 15:53:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:56:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:58:41] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:00:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:03:08] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:05:04] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:06:47] Joining segment hits
[2019-07-05 16:14:02] Reporting output tracks
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[2019-07-05 17:33:28] A summary of the alignment counts can be found in /scratch/7534484.1.linga/tophat2/align_summary.txt
[2019-07-05 17:33:28] Run complete: 06:21:37 elapsed