[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 13:26:53] Preparing reads
	 left reads: min. length=150, max. length=150, 21498225 kept reads (326 discarded)
	right reads: min. length=150, max. length=150, 21498434 kept reads (117 discarded)
[2019-06-28 13:53:26] Building transcriptome data files /scratch/7287277.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:53:47] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:01:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:20:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:39:35] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:39:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:15:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:19:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:24:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:29:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 15:34:02] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 15:38:05] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 15:40:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:22:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 16:27:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 16:32:34] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:38:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:44:34] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:49:16] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:51:43] Searching for junctions via segment mapping
[2019-06-28 18:34:13] Retrieving sequences for splices
[2019-06-28 18:36:44] Indexing splices
[2019-06-28 18:37:54] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 18:39:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 18:42:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 18:44:15] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 18:46:32] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 18:48:11] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 18:48:52] Joining segment hits
[2019-06-28 18:56:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 18:58:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 19:00:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 19:03:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 19:05:17] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 19:06:59] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 19:07:42] Joining segment hits
[2019-06-28 19:15:39] Reporting output tracks
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[2019-06-28 19:53:01] A summary of the alignment counts can be found in /scratch/7287277.1.linga/tophat2/align_summary.txt
[2019-06-28 19:53:01] Run complete: 06:26:18 elapsed