[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 13:25:42] Reading known junctions from GTF file
[2019-06-28 13:25:46] Preparing reads
	 left reads: min. length=150, max. length=150, 23051089 kept reads (352 discarded)
	right reads: min. length=150, max. length=150, 23051339 kept reads (102 discarded)
[2019-06-28 13:54:31] Building transcriptome data files /scratch/7287267.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:54:51] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:01:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:28:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:56:03] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:56:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:39:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:46:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:54:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:02:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:10:57] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:17:22] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:19:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 17:05:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 17:13:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 17:25:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 17:38:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 17:47:55] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:55:42] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:58:59] Searching for junctions via segment mapping
[2019-06-29 05:15:31] Retrieving sequences for splices
[2019-06-29 05:18:13] Indexing splices
[2019-06-29 05:20:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 05:29:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 05:38:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 05:47:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 05:58:56] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 06:07:01] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 06:09:28] Joining segment hits
[2019-06-29 06:29:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 06:39:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 06:50:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 07:00:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 07:09:59] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 07:19:58] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 07:22:04] Joining segment hits
[2019-06-29 07:45:53] Reporting output tracks
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[2019-06-29 09:17:50] A summary of the alignment counts can be found in /scratch/7287267.1.linga/tophat2/align_summary.txt
[2019-06-29 09:17:50] Run complete: 19:52:13 elapsed