[2018-07-14 20:24:18] Beginning TopHat run (v2.1.1)
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[2018-07-14 20:24:18] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:24:18] Checking for Bowtie index files (genome)..
[2018-07-14 20:24:18] Checking for reference FASTA file
[2018-07-14 20:24:18] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:24:25] Reading known junctions from GTF file
[2018-07-14 20:24:31] Preparing reads
	 left reads: min. length=151, max. length=151, 20463935 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 20463536 kept reads (399 discarded)
[2018-07-14 21:02:06] Building transcriptome data files /scratch/6936777.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 21:02:30] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 21:12:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:41:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 22:11:47] Resuming TopHat pipeline with unmapped reads
[2018-07-14 22:11:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:43:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:57:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 23:10:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 23:23:35] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 23:35:38] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 23:43:32] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:48:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-15 00:20:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-15 00:35:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-15 00:50:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-15 01:04:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-15 01:17:41] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-15 01:25:53] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-15 01:31:01] Searching for junctions via segment mapping
[2018-07-15 11:29:44] Retrieving sequences for splices
[2018-07-15 11:32:04] Indexing splices
[2018-07-15 11:32:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 11:43:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 11:54:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 12:07:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 12:19:24] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 12:26:56] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 12:28:30] Joining segment hits
[2018-07-15 12:36:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 12:48:20] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 12:59:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 13:14:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 13:25:20] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 13:32:38] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 13:34:33] Joining segment hits
[2018-07-15 13:42:56] Reporting output tracks
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[2018-07-15 14:37:06] A summary of the alignment counts can be found in /scratch/6936777.1.linga/tophat2/align_summary.txt
[2018-07-15 14:37:06] Run complete: 18:12:48 elapsed