[2019-07-05 11:19:08] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:19:08] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:19:08] Checking for Bowtie index files (genome)..
[2019-07-05 11:19:08] Checking for reference FASTA file
[2019-07-05 11:19:08] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:19:12] Reading known junctions from GTF file
[2019-07-05 11:19:16] Preparing reads
	 left reads: min. length=150, max. length=150, 24805529 kept reads (2009 discarded)
	right reads: min. length=150, max. length=150, 24790591 kept reads (16947 discarded)
[2019-07-05 11:47:02] Building transcriptome data files /scratch/7534476.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:47:18] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:54:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:19:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:45:46] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:45:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:04:34] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:05:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:07:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:09:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:10:39] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:12:13] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:13:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:37:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:39:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:42:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:45:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:48:06] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:50:39] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:53:12] Searching for junctions via segment mapping
[2019-07-05 15:48:12] Retrieving sequences for splices
[2019-07-05 15:50:22] Indexing splices
[2019-07-05 15:52:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:53:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:54:36] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:55:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:57:08] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:58:20] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:59:24] Joining segment hits
[2019-07-05 16:04:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:06:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:08:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:10:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:12:11] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:14:00] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:15:33] Joining segment hits
[2019-07-05 16:22:05] Reporting output tracks
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[2019-07-05 17:38:04] A summary of the alignment counts can be found in /scratch/7534476.1.linga/tophat2/align_summary.txt
[2019-07-05 17:38:04] Run complete: 06:18:56 elapsed