[2019-06-28 13:26:43] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:26:43] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:26:44] Checking for Bowtie index files (genome)..
[2019-06-28 13:26:44] Checking for reference FASTA file
[2019-06-28 13:26:44] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:26:49] Reading known junctions from GTF file
[2019-06-28 13:26:52] Preparing reads
	 left reads: min. length=150, max. length=150, 22674373 kept reads (409 discarded)
	right reads: min. length=150, max. length=150, 22674675 kept reads (107 discarded)
[2019-06-28 13:53:18] Building transcriptome data files /scratch/7287279.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:53:38] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:00:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:20:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:41:10] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:41:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:19:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:24:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:29:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:35:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 15:41:00] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 15:46:31] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 15:49:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:32:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 16:39:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 16:45:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:51:25] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:57:12] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:03:14] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:06:13] Searching for junctions via segment mapping
[2019-06-28 19:28:28] Retrieving sequences for splices
[2019-06-28 19:30:58] Indexing splices
[2019-06-28 19:31:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 19:34:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 19:37:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 19:39:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 19:42:25] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 19:44:25] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 19:45:07] Joining segment hits
[2019-06-28 19:53:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 19:56:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 19:58:59] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 20:01:39] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 20:04:17] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 20:06:18] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 20:07:02] Joining segment hits
[2019-06-28 20:15:19] Reporting output tracks
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[2019-06-28 20:54:50] A summary of the alignment counts can be found in /scratch/7287279.1.linga/tophat2/align_summary.txt
[2019-06-28 20:54:50] Run complete: 07:28:07 elapsed