[2018-07-14 20:29:52] Beginning TopHat run (v2.1.1)
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[2018-07-14 20:29:52] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:29:53] Checking for Bowtie index files (genome)..
[2018-07-14 20:29:53] Checking for reference FASTA file
[2018-07-14 20:29:53] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:29:57] Reading known junctions from GTF file
[2018-07-14 20:30:01] Preparing reads
	 left reads: min. length=151, max. length=151, 15406668 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 15406415 kept reads (253 discarded)
[2018-07-14 20:46:05] Building transcriptome data files /scratch/6936773.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:46:24] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:54:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:09:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:24:57] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:24:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:48:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 21:54:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:01:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:08:30] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:15:22] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:20:28] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:24:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:50:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 23:00:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 23:07:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 23:14:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 23:20:47] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 23:24:48] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:27:14] Searching for junctions via segment mapping
[2018-07-15 06:55:10] Retrieving sequences for splices
[2018-07-15 06:57:26] Indexing splices
[2018-07-15 06:58:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 07:05:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 07:12:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 07:18:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 07:24:50] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 07:28:41] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 07:29:29] Joining segment hits
[2018-07-15 07:36:23] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 07:44:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 07:52:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 07:59:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 08:06:20] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 08:10:27] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 08:11:23] Joining segment hits
[2018-07-15 08:18:20] Reporting output tracks
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[2018-07-15 09:00:25] A summary of the alignment counts can be found in /scratch/6936773.1.linga/tophat2/align_summary.txt
[2018-07-15 09:00:25] Run complete: 12:30:32 elapsed