[2019-09-04 11:22:00] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:22:00] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:22:01] Checking for Bowtie index files (genome)..
[2019-09-04 11:22:01] Checking for reference FASTA file
[2019-09-04 11:22:01] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:22:07] Reading known junctions from GTF file
[2019-09-04 11:22:13] Preparing reads
	 left reads: min. length=150, max. length=150, 28463843 kept reads (6 discarded)
	right reads: min. length=150, max. length=150, 28462774 kept reads (1075 discarded)
[2019-09-04 11:48:50] Building transcriptome data files /scratch/9142554.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:49:07] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:56:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:17:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:41:26] Resuming TopHat pipeline with unmapped reads
[2019-09-04 12:41:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:43:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 13:50:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 13:57:51] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 14:05:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 14:12:21] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 14:18:09] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 14:21:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 15:17:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 15:24:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:32:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 15:39:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 15:47:08] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 15:53:25] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 15:56:53] Searching for junctions via segment mapping
[2019-09-04 16:24:18] Retrieving sequences for splices
[2019-09-04 16:26:42] Indexing splices
[2019-09-04 16:28:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 16:30:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 16:32:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 16:35:02] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 16:37:23] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 16:39:21] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 16:40:57] Joining segment hits
[2019-09-04 16:49:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 16:51:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 16:53:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 16:55:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 16:58:07] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:00:10] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:01:39] Joining segment hits
[2019-09-04 17:10:05] Reporting output tracks
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[2019-09-04 17:50:45] A summary of the alignment counts can be found in /scratch/9142554.1.linga/tophat2/align_summary.txt
[2019-09-04 17:50:45] Run complete: 06:28:45 elapsed