[2019-07-03 18:08:37] Beginning TopHat run (v2.1.1)
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[2019-07-03 18:08:37] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 18:08:37] Checking for Bowtie index files (genome)..
[2019-07-03 18:08:37] Checking for reference FASTA file
[2019-07-03 18:08:37] Generating SAM header for Bowtie2Index/genome
[2019-07-03 18:08:40] Reading known junctions from GTF file
[2019-07-03 18:08:44] Preparing reads
	 left reads: min. length=150, max. length=150, 29402300 kept reads (381 discarded)
	right reads: min. length=150, max. length=150, 29402608 kept reads (73 discarded)
[2019-07-03 18:40:07] Building transcriptome data files /scratch/7505706.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 18:40:23] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 18:46:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:05:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:25:31] Resuming TopHat pipeline with unmapped reads
[2019-07-03 19:25:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 20:22:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:31:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:41:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:51:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 21:01:13] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 21:07:36] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 21:10:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 22:18:41] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 22:29:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 22:39:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:50:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 23:01:09] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 23:08:37] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 23:12:46] Searching for junctions via segment mapping
[2019-07-04 05:10:41] Retrieving sequences for splices
[2019-07-04 05:13:06] Indexing splices
[2019-07-04 05:13:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 05:21:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 05:28:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 05:35:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 05:42:46] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 05:47:05] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 05:48:13] Joining segment hits
[2019-07-04 06:02:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 06:09:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 06:17:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 06:25:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 06:32:05] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 06:36:22] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 06:37:35] Joining segment hits
[2019-07-04 06:51:18] Reporting output tracks
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[2019-07-04 07:41:14] A summary of the alignment counts can be found in /scratch/7505706.1.linga/tophat2/align_summary.txt
[2019-07-04 07:41:14] Run complete: 13:32:37 elapsed