[2018-07-14 20:20:47] Beginning TopHat run (v2.1.1)
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[2018-07-14 20:20:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:20:47] Checking for Bowtie index files (genome)..
[2018-07-14 20:20:47] Checking for reference FASTA file
[2018-07-14 20:20:47] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:20:52] Reading known junctions from GTF file
[2018-07-14 20:20:56] Preparing reads
	 left reads: min. length=151, max. length=151, 16046055 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 16045746 kept reads (309 discarded)
[2018-07-14 20:40:44] Building transcriptome data files /scratch/6936774.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:41:04] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:50:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:05:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:22:12] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:22:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:44:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 21:50:45] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 21:58:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:05:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:11:58] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:16:07] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:18:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:41:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:48:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:55:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 23:02:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 23:09:36] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 23:14:22] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:17:00] Searching for junctions via segment mapping
[2018-07-15 06:15:39] Retrieving sequences for splices
[2018-07-15 06:17:58] Indexing splices
[2018-07-15 06:18:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 06:24:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 06:30:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 06:36:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 06:41:46] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 06:44:48] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 06:45:23] Joining segment hits
[2018-07-15 06:51:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 06:56:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 07:02:09] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 07:07:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 07:12:29] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 07:15:35] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 07:16:22] Joining segment hits
[2018-07-15 07:22:11] Reporting output tracks
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[2018-07-15 07:52:41] A summary of the alignment counts can be found in /scratch/6936774.1.linga/tophat2/align_summary.txt
[2018-07-15 07:52:41] Run complete: 11:31:54 elapsed