[2018-07-14 20:20:53] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-07-14 20:20:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:20:53] Checking for Bowtie index files (genome)..
[2018-07-14 20:20:53] Checking for reference FASTA file
[2018-07-14 20:20:53] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:20:57] Reading known junctions from GTF file
[2018-07-14 20:21:01] Preparing reads
	 left reads: min. length=151, max. length=151, 12587531 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 12587298 kept reads (233 discarded)
[2018-07-14 20:33:01] Building transcriptome data files /scratch/6936768.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:33:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:41:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 20:55:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:09:36] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:09:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:26:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 21:34:12] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 21:41:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 21:49:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 21:57:13] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:01:47] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:04:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:26:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:35:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:43:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:51:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:58:53] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 23:04:05] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:07:05] Searching for junctions via segment mapping
[2018-07-15 09:20:14] Retrieving sequences for splices
[2018-07-15 09:22:31] Indexing splices
[2018-07-15 09:23:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 09:33:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 09:43:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 09:53:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 10:01:35] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 10:06:08] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 10:07:01] Joining segment hits
[2018-07-15 10:14:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 10:24:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 10:34:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 10:44:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 10:53:32] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 10:58:37] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 10:59:38] Joining segment hits
[2018-07-15 11:06:11] Reporting output tracks
-----------------------------------------------
[2018-07-15 12:05:51] A summary of the alignment counts can be found in /scratch/6936768.1.linga/tophat2/align_summary.txt
[2018-07-15 12:05:51] Run complete: 15:44:58 elapsed