[2018-07-14 20:21:14] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-07-14 20:21:14] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:21:15] Checking for Bowtie index files (genome)..
[2018-07-14 20:21:15] Checking for reference FASTA file
[2018-07-14 20:21:15] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:21:18] Reading known junctions from GTF file
[2018-07-14 20:21:23] Preparing reads
	 left reads: min. length=151, max. length=151, 14266513 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 14266187 kept reads (326 discarded)
[2018-07-14 20:34:55] Building transcriptome data files /scratch/6936771.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:35:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:43:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 20:58:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:14:09] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:14:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 21:37:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 21:45:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 21:54:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:04:30] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:12:55] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:18:13] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:22:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:50:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 23:00:39] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 23:09:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 23:18:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 23:27:12] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 23:33:32] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:37:44] Searching for junctions via segment mapping
[2018-07-15 07:29:32] Retrieving sequences for splices
[2018-07-15 07:31:45] Indexing splices
[2018-07-15 07:32:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 07:42:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 07:52:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 08:02:44] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 08:11:19] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 08:16:17] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 08:17:31] Joining segment hits
[2018-07-15 08:24:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 08:35:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 08:47:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 08:58:03] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 09:06:58] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 09:12:00] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 09:13:21] Joining segment hits
[2018-07-15 09:20:30] Reporting output tracks
-----------------------------------------------
[2018-07-15 10:19:31] A summary of the alignment counts can be found in /scratch/6936771.1.linga/tophat2/align_summary.txt
[2018-07-15 10:19:31] Run complete: 13:58:17 elapsed