[2018-10-12 23:12:40] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:12:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:12:40] Checking for Bowtie index files (genome)..
[2018-10-12 23:12:40] Checking for reference FASTA file
[2018-10-12 23:12:40] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:12:43] Reading known junctions from GTF file
[2018-10-12 23:12:45] Preparing reads
	 left reads: min. length=100, max. length=100, 635005 kept reads (349 discarded)
	right reads: min. length=100, max. length=100, 634621 kept reads (733 discarded)
[2018-10-12 23:13:04] Building transcriptome data files /scratch/8792829.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:13:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:18:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:19:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:19:49] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:19:49] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:20:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:20:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:20:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:20:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:20:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:21:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:21:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:21:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:21:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:21:55] Searching for junctions via segment mapping
[2018-10-12 23:23:30] Retrieving sequences for splices
[2018-10-12 23:24:43] Indexing splices
[2018-10-12 23:24:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:24:58] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:25:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:25:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:25:05] Joining segment hits
[2018-10-12 23:26:23] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:26:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:26:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:26:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:26:33] Joining segment hits
[2018-10-12 23:27:57] Reporting output tracks
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[2018-10-12 23:30:10] A summary of the alignment counts can be found in /scratch/8792829.1.c/tophat2/align_summary.txt
[2018-10-12 23:30:10] Run complete: 00:17:29 elapsed