[2018-10-13 11:03:40] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:03:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:03:40] Checking for Bowtie index files (genome)..
[2018-10-13 11:03:40] Checking for reference FASTA file
[2018-10-13 11:03:40] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:03:44] Reading known junctions from GTF file
[2018-10-13 11:03:48] Preparing reads
	 left reads: min. length=100, max. length=100, 589252 kept reads (230 discarded)
	right reads: min. length=100, max. length=100, 588902 kept reads (580 discarded)
[2018-10-13 11:04:13] Building transcriptome data files /scratch/8793191.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:04:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:12:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:13:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:13:45] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:13:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:14:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:14:20] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:14:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:14:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:14:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:15:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:15:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:15:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:15:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:16:01] Searching for junctions via segment mapping
[2018-10-13 11:19:31] Retrieving sequences for splices
[2018-10-13 11:21:33] Indexing splices
[2018-10-13 11:21:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:21:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:22:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:22:07] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:22:12] Joining segment hits
[2018-10-13 11:24:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:24:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:24:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:24:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:24:54] Joining segment hits
[2018-10-13 11:27:21] Reporting output tracks
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[2018-10-13 11:33:43] A summary of the alignment counts can be found in /scratch/8793191.1.linga/tophat2/align_summary.txt
[2018-10-13 11:33:43] Run complete: 00:30:03 elapsed