[2018-07-14 20:20:38] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-07-14 20:20:38] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:20:39] Checking for Bowtie index files (genome)..
[2018-07-14 20:20:39] Checking for reference FASTA file
[2018-07-14 20:20:39] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:20:42] Reading known junctions from GTF file
[2018-07-14 20:20:46] Preparing reads
	 left reads: min. length=151, max. length=151, 16837804 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 16837476 kept reads (328 discarded)
[2018-07-14 20:39:08] Building transcriptome data files /scratch/6936776.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:39:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:47:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:01:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:15:28] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:15:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:38:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 21:44:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 21:49:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 21:55:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:01:08] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:04:39] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:07:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:29:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:36:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:43:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:49:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:55:30] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:59:26] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:01:54] Searching for junctions via segment mapping
[2018-07-15 03:24:37] Retrieving sequences for splices
[2018-07-15 03:26:34] Indexing splices
[2018-07-15 03:27:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 03:31:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 03:36:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 03:40:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 03:44:39] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 03:47:11] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 03:47:52] Joining segment hits
[2018-07-15 03:53:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 03:58:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 04:03:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 04:07:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 04:11:59] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 04:14:38] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 04:15:22] Joining segment hits
[2018-07-15 04:21:25] Reporting output tracks
-----------------------------------------------
[2018-07-15 04:59:12] A summary of the alignment counts can be found in /scratch/6936776.1.linga/tophat2/align_summary.txt
[2018-07-15 04:59:12] Run complete: 08:38:33 elapsed