[2019-07-05 10:58:57] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-05 10:58:57] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 10:58:57] Checking for Bowtie index files (genome)..
[2019-07-05 10:58:57] Checking for reference FASTA file
[2019-07-05 10:58:57] Generating SAM header for Bowtie2Index/genome
[2019-07-05 10:58:59] Reading known junctions from GTF file
[2019-07-05 10:59:02] Preparing reads
	 left reads: min. length=150, max. length=150, 23955399 kept reads (1869 discarded)
	right reads: min. length=150, max. length=150, 23940822 kept reads (16446 discarded)
[2019-07-05 11:18:59] Building transcriptome data files /scratch/7534470.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:19:07] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:22:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:35:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:49:52] Resuming TopHat pipeline with unmapped reads
[2019-07-05 11:49:53] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 11:58:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 11:59:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 11:59:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:00:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:01:26] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:02:14] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:02:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:13:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:14:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:15:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:16:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:18:12] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:19:21] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:20:32] Searching for junctions via segment mapping
[2019-07-05 13:21:47] Retrieving sequences for splices
[2019-07-05 13:22:53] Indexing splices
[2019-07-05 13:23:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:24:26] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:25:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:25:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:26:34] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:27:15] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:27:50] Joining segment hits
[2019-07-05 13:30:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:31:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:32:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:33:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:34:30] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:35:27] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:36:20] Joining segment hits
[2019-07-05 13:39:24] Reporting output tracks
-----------------------------------------------
[2019-07-05 14:21:25] A summary of the alignment counts can be found in /scratch/7534470.1.linga/tophat2/align_summary.txt
[2019-07-05 14:21:25] Run complete: 03:22:28 elapsed