[2018-10-13 16:00:47] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:00:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:00:47] Checking for Bowtie index files (genome)..
[2018-10-13 16:00:47] Checking for reference FASTA file
[2018-10-13 16:00:47] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:00:53] Reading known junctions from GTF file
[2018-10-13 16:00:59] Preparing reads
	 left reads: min. length=100, max. length=100, 150538 kept reads (143 discarded)
	right reads: min. length=100, max. length=100, 150444 kept reads (237 discarded)
[2018-10-13 16:01:07] Building transcriptome data files /scratch/8793342.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:01:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:11:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:11:32] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:11:56] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:11:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:12:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:12:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:12:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:12:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:13:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:13:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:13:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:13:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:13:57] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:14:06] Searching for junctions via segment mapping
[2018-10-13 16:17:14] Retrieving sequences for splices
[2018-10-13 16:20:06] Indexing splices
[2018-10-13 16:20:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:20:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:20:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:20:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:20:50] Joining segment hits
[2018-10-13 16:23:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:23:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:23:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:23:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:23:38] Joining segment hits
[2018-10-13 16:26:20] Reporting output tracks
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[2018-10-13 16:29:27] A summary of the alignment counts can be found in /scratch/8793342.1.linga/tophat2/align_summary.txt
[2018-10-13 16:29:27] Run complete: 00:28:39 elapsed