[2018-10-13 15:07:30] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:07:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:07:30] Checking for Bowtie index files (genome)..
[2018-10-13 15:07:30] Checking for reference FASTA file
[2018-10-13 15:07:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:07:35] Reading known junctions from GTF file
[2018-10-13 15:07:39] Preparing reads
	 left reads: min. length=100, max. length=100, 1411797 kept reads (93 discarded)
	right reads: min. length=100, max. length=100, 1411219 kept reads (671 discarded)
[2018-10-13 15:08:58] Building transcriptome data files /scratch/8793312.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:09:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:18:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:20:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:21:25] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:21:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:22:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:22:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:22:34] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:22:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:23:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:24:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:24:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:24:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:24:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:25:02] Searching for junctions via segment mapping
[2018-10-13 15:30:07] Retrieving sequences for splices
[2018-10-13 15:33:05] Indexing splices
[2018-10-13 15:33:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:33:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:33:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:34:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:34:09] Joining segment hits
[2018-10-13 15:36:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:36:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:37:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:37:08] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:37:14] Joining segment hits
[2018-10-13 15:40:59] Reporting output tracks
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[2018-10-13 15:53:24] A summary of the alignment counts can be found in /scratch/8793312.1.linga/tophat2/align_summary.txt
[2018-10-13 15:53:24] Run complete: 00:45:53 elapsed