[2019-06-28 13:25:37] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:25:37] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:25:37] Checking for Bowtie index files (genome)..
[2019-06-28 13:25:37] Checking for reference FASTA file
[2019-06-28 13:25:37] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:25:43] Reading known junctions from GTF file
[2019-06-28 13:25:46] Preparing reads
	 left reads: min. length=150, max. length=150, 29893535 kept reads (568 discarded)
	right reads: min. length=150, max. length=150, 29893964 kept reads (139 discarded)
[2019-06-28 14:01:53] Building transcriptome data files /scratch/7287268.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 14:02:14] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:10:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:45:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 15:20:24] Resuming TopHat pipeline with unmapped reads
[2019-06-28 15:20:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:22:35] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 16:31:43] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 16:41:51] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:51:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 17:02:01] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:09:28] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:12:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 18:18:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 18:32:43] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 18:45:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 18:57:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 19:10:16] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 19:19:39] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 19:24:28] Searching for junctions via segment mapping
[2019-06-29 10:03:23] Retrieving sequences for splices
[2019-06-29 10:05:48] Indexing splices
[2019-06-29 10:07:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 10:17:59] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 10:29:26] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 10:42:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 10:53:52] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 11:02:59] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 11:05:35] Joining segment hits
[2019-06-29 11:25:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 11:37:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 11:49:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 12:01:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 12:11:31] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 12:19:29] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 12:21:42] Joining segment hits
[2019-06-29 12:41:36] Reporting output tracks
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[2019-06-29 14:43:48] A summary of the alignment counts can be found in /scratch/7287268.1.linga/tophat2/align_summary.txt
[2019-06-29 14:43:48] Run complete: 1 days 01:18:11 elapsed