[2019-07-05 11:18:21] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:18:21] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:18:22] Checking for Bowtie index files (genome)..
[2019-07-05 11:18:22] Checking for reference FASTA file
[2019-07-05 11:18:22] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:18:24] Reading known junctions from GTF file
[2019-07-05 11:18:28] Preparing reads
	 left reads: min. length=150, max. length=150, 26045107 kept reads (2004 discarded)
	right reads: min. length=150, max. length=150, 26029277 kept reads (17834 discarded)
[2019-07-05 11:47:56] Building transcriptome data files /scratch/7534471.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:48:12] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:54:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:19:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:47:33] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:47:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:09:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:10:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:12:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:14:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:16:14] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:18:02] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:19:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:45:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:47:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:49:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:52:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:55:20] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:57:57] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 14:00:26] Searching for junctions via segment mapping
[2019-07-05 16:23:46] Retrieving sequences for splices
[2019-07-05 16:26:39] Indexing splices
[2019-07-05 16:28:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:30:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:31:36] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:33:07] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:34:41] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:36:12] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:37:31] Joining segment hits
[2019-07-05 16:44:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:46:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:48:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:51:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:53:29] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:55:31] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:57:28] Joining segment hits
[2019-07-05 17:04:48] Reporting output tracks
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[2019-07-05 18:47:15] A summary of the alignment counts can be found in /scratch/7534471.1.linga/tophat2/align_summary.txt
[2019-07-05 18:47:15] Run complete: 07:28:54 elapsed