[2019-07-05 15:20:38] Beginning TopHat run (v2.1.1)
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[2019-07-05 15:20:38] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 15:20:38] Checking for Bowtie index files (genome)..
[2019-07-05 15:20:38] Checking for reference FASTA file
[2019-07-05 15:20:38] Generating SAM header for Bowtie2Index/genome
[2019-07-05 15:20:46] Reading known junctions from GTF file
[2019-07-05 15:20:53] Preparing reads
	 left reads: min. length=150, max. length=150, 25776983 kept reads (1826 discarded)
	right reads: min. length=150, max. length=150, 25759418 kept reads (19391 discarded)
[2019-07-05 16:00:59] Building transcriptome data files /scratch/7534492.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 16:01:23] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 16:13:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 16:53:22] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 17:33:56] Resuming TopHat pipeline with unmapped reads
[2019-07-05 17:33:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 17:57:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 17:59:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 18:02:24] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 18:04:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 18:07:36] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 18:09:59] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 18:12:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 18:38:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 18:42:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 18:46:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 18:50:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 18:54:13] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 18:58:21] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 19:01:46] Searching for junctions via segment mapping
[2019-07-05 22:36:19] Retrieving sequences for splices
[2019-07-05 22:41:29] Indexing splices
[2019-07-05 22:45:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 22:47:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 22:49:53] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 22:52:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 22:54:48] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 22:57:13] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 22:59:13] Joining segment hits
[2019-07-05 23:06:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 23:10:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 23:14:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 23:17:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 23:21:18] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 23:24:31] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 23:27:23] Joining segment hits
[2019-07-05 23:39:55] Reporting output tracks
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[2019-07-06 01:49:57] A summary of the alignment counts can be found in /scratch/7534492.1.linga/tophat2/align_summary.txt
[2019-07-06 01:49:57] Run complete: 10:29:19 elapsed