[2018-10-13 16:55:04] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:55:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:55:04] Checking for Bowtie index files (genome)..
[2018-10-13 16:55:04] Checking for reference FASTA file
[2018-10-13 16:55:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:55:06] Reading known junctions from GTF file
[2018-10-13 16:55:08] Preparing reads
	 left reads: min. length=100, max. length=100, 591082 kept reads (375 discarded)
	right reads: min. length=100, max. length=100, 590697 kept reads (760 discarded)
[2018-10-13 16:55:25] Building transcriptome data files /scratch/8793375.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:55:36] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:00:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:00:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:01:22] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:01:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:01:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:02:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:02:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:02:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:02:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:02:55] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:03:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:03:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:03:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:03:19] Searching for junctions via segment mapping
[2018-10-13 17:04:47] Retrieving sequences for splices
[2018-10-13 17:05:54] Indexing splices
[2018-10-13 17:06:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:06:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:06:10] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:06:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:06:14] Joining segment hits
[2018-10-13 17:07:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:07:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:07:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:07:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:07:42] Joining segment hits
[2018-10-13 17:09:00] Reporting output tracks
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[2018-10-13 17:11:14] A summary of the alignment counts can be found in /scratch/8793375.1.p16/tophat2/align_summary.txt
[2018-10-13 17:11:14] Run complete: 00:16:10 elapsed