[2018-10-13 17:03:12] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:03:12] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:03:12] Checking for Bowtie index files (genome)..
[2018-10-13 17:03:12] Checking for reference FASTA file
[2018-10-13 17:03:12] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:03:16] Reading known junctions from GTF file
[2018-10-13 17:03:21] Preparing reads
	 left reads: min. length=100, max. length=100, 187252 kept reads (319 discarded)
	right reads: min. length=100, max. length=100, 187114 kept reads (457 discarded)
[2018-10-13 17:03:29] Building transcriptome data files /scratch/8793384.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:03:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:12:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:12:26] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:12:50] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:12:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:13:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:13:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:13:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:13:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:13:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:14:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:14:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:14:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:14:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:14:51] Searching for junctions via segment mapping
[2018-10-13 17:17:15] Retrieving sequences for splices
[2018-10-13 17:19:16] Indexing splices
[2018-10-13 17:19:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:19:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:19:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:19:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:19:53] Joining segment hits
[2018-10-13 17:21:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:22:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:22:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:22:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:22:15] Joining segment hits
[2018-10-13 17:24:22] Reporting output tracks
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[2018-10-13 17:26:59] A summary of the alignment counts can be found in /scratch/8793384.1.linga/tophat2/align_summary.txt
[2018-10-13 17:26:59] Run complete: 00:23:46 elapsed