[2018-10-13 17:29:43] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:29:43] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:29:43] Checking for Bowtie index files (genome)..
[2018-10-13 17:29:43] Checking for reference FASTA file
[2018-10-13 17:29:43] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:29:48] Reading known junctions from GTF file
[2018-10-13 17:29:52] Preparing reads
	 left reads: min. length=100, max. length=100, 178704 kept reads (80 discarded)
	right reads: min. length=100, max. length=100, 178616 kept reads (168 discarded)
[2018-10-13 17:30:00] Building transcriptome data files /scratch/8793400.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:30:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:38:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:38:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:39:05] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:39:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:39:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:39:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:39:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:39:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:39:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:40:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:40:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:40:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:40:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:40:43] Searching for junctions via segment mapping
[2018-10-13 17:43:32] Retrieving sequences for splices
[2018-10-13 17:45:48] Indexing splices
[2018-10-13 17:46:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:46:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:46:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:46:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:46:24] Joining segment hits
[2018-10-13 17:48:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:48:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:48:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:48:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:48:58] Joining segment hits
[2018-10-13 17:51:19] Reporting output tracks
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[2018-10-13 17:54:14] A summary of the alignment counts can be found in /scratch/8793400.1.linga/tophat2/align_summary.txt
[2018-10-13 17:54:14] Run complete: 00:24:31 elapsed