[2019-07-13 02:49:09] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-13 02:49:09] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-13 02:49:09] Checking for Bowtie index files (genome)..
[2019-07-13 02:49:09] Checking for reference FASTA file
[2019-07-13 02:49:09] Generating SAM header for Bowtie2Index/genome
[2019-07-13 02:49:10] Reading known junctions from GTF file
[2019-07-13 02:49:12] Preparing reads
	 left reads: min. length=150, max. length=150, 80976020 kept reads (7383 discarded)
	right reads: min. length=150, max. length=150, 80963148 kept reads (20255 discarded)
[2019-07-13 03:38:19] Building transcriptome data files /scratch/7682060.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-13 03:38:28] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-13 03:42:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-13 04:22:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-13 05:03:37] Resuming TopHat pipeline with unmapped reads
[2019-07-13 05:03:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 06:08:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 06:19:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 06:31:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 06:42:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 06:53:43] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 07:02:11] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 07:07:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 08:16:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 08:28:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 08:39:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 08:52:07] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 09:03:31] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 09:12:35] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 09:18:44] Searching for junctions via segment mapping
[2019-07-13 16:37:27] Retrieving sequences for splices
[2019-07-13 16:38:38] Indexing splices
[2019-07-13 16:39:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 16:46:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 16:54:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 17:02:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 17:09:27] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 17:14:55] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 17:17:04] Joining segment hits
[2019-07-13 17:28:16] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 17:36:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 17:44:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 17:52:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 18:00:30] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 18:05:42] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 18:07:55] Joining segment hits
[2019-07-13 18:20:01] Reporting output tracks
-----------------------------------------------
[2019-07-13 19:31:00] A summary of the alignment counts can be found in /scratch/7682060.1.p16/tophat2/align_summary.txt
[2019-07-13 19:31:00] Run complete: 16:41:51 elapsed