[2018-10-13 15:02:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:02:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:02:03] Checking for Bowtie index files (genome)..
[2018-10-13 15:02:03] Checking for reference FASTA file
[2018-10-13 15:02:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:02:05] Reading known junctions from GTF file
[2018-10-13 15:02:07] Preparing reads
	 left reads: min. length=100, max. length=100, 825855 kept reads (91 discarded)
	right reads: min. length=100, max. length=100, 825579 kept reads (367 discarded)
[2018-10-13 15:02:31] Building transcriptome data files /scratch/8793307.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:02:41] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:08:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:09:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:09:35] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:09:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:09:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:10:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:10:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:10:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:10:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:10:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:10:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:10:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:11:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:11:09] Searching for junctions via segment mapping
[2018-10-13 15:12:53] Retrieving sequences for splices
[2018-10-13 15:14:06] Indexing splices
[2018-10-13 15:14:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:14:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:14:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:14:25] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:14:27] Joining segment hits
[2018-10-13 15:15:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:15:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:15:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:15:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:15:58] Joining segment hits
[2018-10-13 15:17:20] Reporting output tracks
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[2018-10-13 15:19:59] A summary of the alignment counts can be found in /scratch/8793307.1.c/tophat2/align_summary.txt
[2018-10-13 15:19:59] Run complete: 00:17:56 elapsed