[2019-07-17 19:08:08] Beginning TopHat run (v2.1.1)
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[2019-07-17 19:08:08] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 19:08:08] Checking for Bowtie index files (genome)..
[2019-07-17 19:08:08] Checking for reference FASTA file
[2019-07-17 19:08:08] Generating SAM header for Bowtie2Index/genome
[2019-07-17 19:08:10] Reading known junctions from GTF file
[2019-07-17 19:08:14] Preparing reads
	 left reads: min. length=150, max. length=150, 62881296 kept reads (5644 discarded)
	right reads: min. length=150, max. length=150, 62871522 kept reads (15418 discarded)
[2019-07-17 19:54:39] Building transcriptome data files /scratch/7775058.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 19:54:48] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 19:58:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 20:24:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 20:52:20] Resuming TopHat pipeline with unmapped reads
[2019-07-17 20:52:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 21:36:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-17 21:44:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-17 21:52:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-17 22:01:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-17 22:09:21] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-17 22:15:32] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-17 22:18:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 23:07:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-17 23:16:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-17 23:24:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-17 23:33:55] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-17 23:42:47] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-17 23:49:32] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-17 23:53:33] Searching for junctions via segment mapping
[2019-07-18 06:25:25] Retrieving sequences for splices
[2019-07-18 06:26:31] Indexing splices
[2019-07-18 06:27:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 06:33:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 06:40:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 06:47:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 06:54:14] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 06:59:12] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 07:00:30] Joining segment hits
[2019-07-18 07:09:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 07:16:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 07:23:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 07:30:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 07:37:27] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 07:42:12] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 07:43:24] Joining segment hits
[2019-07-18 07:52:46] Reporting output tracks
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[2019-07-18 09:02:20] A summary of the alignment counts can be found in /scratch/7775058.1.linga/tophat2/align_summary.txt
[2019-07-18 09:02:20] Run complete: 13:54:11 elapsed