[2019-06-24 17:40:50] Beginning TopHat run (v2.1.1)
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[2019-06-24 17:40:50] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 17:40:50] Checking for Bowtie index files (genome)..
[2019-06-24 17:40:50] Checking for reference FASTA file
[2019-06-24 17:40:50] Generating SAM header for Bowtie2Index/genome
[2019-06-24 17:40:55] Reading known junctions from GTF file
[2019-06-24 17:40:58] Preparing reads
	 left reads: min. length=150, max. length=150, 19615410 kept reads (644 discarded)
	right reads: min. length=150, max. length=150, 19613836 kept reads (2218 discarded)
[2019-06-24 18:04:18] Building transcriptome data files /scratch/7056757.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:04:34] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:11:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 18:29:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 18:48:45] Resuming TopHat pipeline with unmapped reads
[2019-06-24 18:48:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:25:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-24 19:29:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-24 19:34:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-24 19:38:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-24 19:42:38] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-24 19:45:47] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-24 19:47:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:29:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-24 20:37:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-24 20:45:01] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-24 20:52:12] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-24 20:58:18] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-24 21:03:12] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-24 21:06:05] Searching for junctions via segment mapping
[2019-06-24 23:57:45] Retrieving sequences for splices
[2019-06-24 23:59:48] Indexing splices
[2019-06-25 00:00:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-25 00:02:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-25 00:05:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-25 00:07:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-25 00:09:37] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-25 00:11:09] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-25 00:11:37] Joining segment hits
[2019-06-25 00:19:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-25 00:21:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-25 00:24:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-25 00:27:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-25 00:30:05] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-25 00:31:54] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-25 00:32:36] Joining segment hits
[2019-06-25 00:40:30] Reporting output tracks
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[2019-06-25 01:57:24] A summary of the alignment counts can be found in /scratch/7056757.1.linga/tophat2/align_summary.txt
[2019-06-25 01:57:24] Run complete: 08:16:34 elapsed