[2018-10-13 16:12:09] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:12:09] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:12:09] Checking for Bowtie index files (genome)..
[2018-10-13 16:12:09] Checking for reference FASTA file
[2018-10-13 16:12:09] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:12:13] Reading known junctions from GTF file
[2018-10-13 16:12:18] Preparing reads
	 left reads: min. length=100, max. length=100, 410017 kept reads (229 discarded)
	right reads: min. length=100, max. length=100, 409642 kept reads (604 discarded)
[2018-10-13 16:12:36] Building transcriptome data files /scratch/8793346.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:12:55] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:20:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:21:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:22:04] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:22:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:22:28] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:22:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:22:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:22:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:23:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:23:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:23:45] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:23:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:24:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:24:20] Searching for junctions via segment mapping
[2018-10-13 16:28:25] Retrieving sequences for splices
[2018-10-13 16:30:36] Indexing splices
[2018-10-13 16:30:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:31:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:31:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:31:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:31:19] Joining segment hits
[2018-10-13 16:33:45] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:33:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:33:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:34:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:34:08] Joining segment hits
[2018-10-13 16:36:32] Reporting output tracks
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[2018-10-13 16:45:04] A summary of the alignment counts can be found in /scratch/8793346.1.linga/tophat2/align_summary.txt
[2018-10-13 16:45:04] Run complete: 00:32:55 elapsed