[2018-10-13 16:14:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:14:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:14:29] Checking for Bowtie index files (genome)..
[2018-10-13 16:14:29] Checking for reference FASTA file
[2018-10-13 16:14:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:14:31] Reading known junctions from GTF file
[2018-10-13 16:14:33] Preparing reads
	 left reads: min. length=100, max. length=100, 528756 kept reads (441 discarded)
	right reads: min. length=100, max. length=100, 528802 kept reads (395 discarded)
[2018-10-13 16:14:49] Building transcriptome data files /scratch/8793349.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:14:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:19:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:20:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:20:29] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:20:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:20:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:20:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:20:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:20:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:21:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:21:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:21:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:21:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:21:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:21:40] Searching for junctions via segment mapping
[2018-10-13 16:23:18] Retrieving sequences for splices
[2018-10-13 16:24:24] Indexing splices
[2018-10-13 16:24:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:24:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:24:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:24:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:24:44] Joining segment hits
[2018-10-13 16:25:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:26:00] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:26:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:26:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:26:08] Joining segment hits
[2018-10-13 16:27:22] Reporting output tracks
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[2018-10-13 16:30:03] A summary of the alignment counts can be found in /scratch/8793349.1.p16/tophat2/align_summary.txt
[2018-10-13 16:30:03] Run complete: 00:15:34 elapsed