[2019-07-05 11:19:33] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:19:33] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:19:33] Checking for Bowtie index files (genome)..
[2019-07-05 11:19:33] Checking for reference FASTA file
[2019-07-05 11:19:33] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:19:37] Reading known junctions from GTF file
[2019-07-05 11:19:40] Preparing reads
	 left reads: min. length=150, max. length=150, 24827164 kept reads (1993 discarded)
	right reads: min. length=150, max. length=150, 24812033 kept reads (17124 discarded)
[2019-07-05 11:47:24] Building transcriptome data files /scratch/7534479.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:47:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:54:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:20:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:48:05] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:48:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:06:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:07:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:09:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:10:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:12:31] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:14:13] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:15:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:38:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:40:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:42:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:45:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:47:39] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:50:10] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:52:34] Searching for junctions via segment mapping
[2019-07-05 16:01:00] Retrieving sequences for splices
[2019-07-05 16:03:29] Indexing splices
[2019-07-05 16:05:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:06:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:07:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:09:07] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:10:22] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:11:35] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:12:40] Joining segment hits
[2019-07-05 16:18:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:20:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:22:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:24:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:26:29] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:28:22] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:30:09] Joining segment hits
[2019-07-05 16:37:25] Reporting output tracks
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[2019-07-05 18:00:49] A summary of the alignment counts can be found in /scratch/7534479.1.linga/tophat2/align_summary.txt
[2019-07-05 18:00:49] Run complete: 06:41:16 elapsed