[2018-10-13 17:01:25] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:01:25] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:01:26] Checking for Bowtie index files (genome)..
[2018-10-13 17:01:26] Checking for reference FASTA file
[2018-10-13 17:01:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:01:30] Reading known junctions from GTF file
[2018-10-13 17:01:34] Preparing reads
	 left reads: min. length=100, max. length=100, 773636 kept reads (515 discarded)
	right reads: min. length=100, max. length=100, 773087 kept reads (1064 discarded)
[2018-10-13 17:02:06] Building transcriptome data files /scratch/8793381.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:02:23] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:10:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:11:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:12:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:12:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:13:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:13:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:13:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:13:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:14:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:14:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:14:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:15:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:15:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:15:36] Searching for junctions via segment mapping
[2018-10-13 17:18:41] Retrieving sequences for splices
[2018-10-13 17:20:42] Indexing splices
[2018-10-13 17:21:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:21:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:21:10] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:21:15] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:21:19] Joining segment hits
[2018-10-13 17:23:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:23:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:23:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:23:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:23:58] Joining segment hits
[2018-10-13 17:26:17] Reporting output tracks
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[2018-10-13 17:30:41] A summary of the alignment counts can be found in /scratch/8793381.1.linga/tophat2/align_summary.txt
[2018-10-13 17:30:41] Run complete: 00:29:15 elapsed