[2018-07-14 20:20:47] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[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 20:20:51] Reading known junctions from GTF file
[2018-07-14 20:20:56] Preparing reads
	 left reads: min. length=151, max. length=151, 15208778 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 15208467 kept reads (311 discarded)
[2018-07-14 20:38:58] Building transcriptome data files /scratch/6936775.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:39:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:48:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:02:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:17:04] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:17:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:42:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 21:48:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 21:57:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:05:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:13:05] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:17:37] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:21:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:45:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:53:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 23:01:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 23:09:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 23:17:39] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 23:22:06] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:25:28] Searching for junctions via segment mapping
[2018-07-15 05:19:08] Retrieving sequences for splices
[2018-07-15 05:21:29] Indexing splices
[2018-07-15 05:22:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 05:29:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 05:36:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 05:43:02] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 05:49:31] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 05:52:53] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 05:53:43] Joining segment hits
[2018-07-15 05:59:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 06:05:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 06:12:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 06:18:23] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 06:24:44] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 06:28:26] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 06:29:28] Joining segment hits
[2018-07-15 06:36:12] Reporting output tracks
-----------------------------------------------
[2018-07-15 07:31:21] A summary of the alignment counts can be found in /scratch/6936775.1.linga/tophat2/align_summary.txt
[2018-07-15 07:31:21] Run complete: 11:10:33 elapsed