[2018-10-13 10:14:22] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:14:22] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:14:22] Checking for Bowtie index files (genome)..
[2018-10-13 10:14:22] Checking for reference FASTA file
[2018-10-13 10:14:22] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:14:24] Reading known junctions from GTF file
[2018-10-13 10:14:27] Preparing reads
	 left reads: min. length=100, max. length=100, 1289213 kept reads (115 discarded)
	right reads: min. length=100, max. length=100, 1288834 kept reads (494 discarded)
[2018-10-13 10:15:02] Building transcriptome data files /scratch/8793170.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:15:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:19:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:20:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:21:07] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:21:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:21:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:21:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:21:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:21:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:21:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:22:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:22:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:22:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:22:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:22:50] Searching for junctions via segment mapping
[2018-10-13 10:25:02] Retrieving sequences for splices
[2018-10-13 10:26:09] Indexing splices
[2018-10-13 10:26:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:26:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:26:26] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:26:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:26:32] Joining segment hits
[2018-10-13 10:27:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:27:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:27:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:27:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:28:00] Joining segment hits
[2018-10-13 10:29:16] Reporting output tracks
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[2018-10-13 10:34:35] A summary of the alignment counts can be found in /scratch/8793170.1.p16/tophat2/align_summary.txt
[2018-10-13 10:34:35] Run complete: 00:20:13 elapsed