[2018-10-13 06:13:28] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:13:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:13:28] Checking for Bowtie index files (genome)..
[2018-10-13 06:13:28] Checking for reference FASTA file
[2018-10-13 06:13:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:13:32] Reading known junctions from GTF file
[2018-10-13 06:13:37] Preparing reads
	 left reads: min. length=100, max. length=100, 656115 kept reads (256 discarded)
	right reads: min. length=100, max. length=100, 655823 kept reads (548 discarded)
[2018-10-13 06:14:03] Building transcriptome data files /scratch/8793050.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:14:23] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:21:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:22:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:23:31] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:23:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:24:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:24:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:24:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:24:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:25:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:25:53] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:26:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:26:18] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:26:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:26:41] Searching for junctions via segment mapping
[2018-10-13 06:29:47] Retrieving sequences for splices
[2018-10-13 06:31:51] Indexing splices
[2018-10-13 06:32:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:32:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:32:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:32:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:32:28] Joining segment hits
[2018-10-13 06:34:55] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:34:59] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:35:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:35:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:35:14] Joining segment hits
[2018-10-13 06:38:07] Reporting output tracks
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[2018-10-13 06:42:46] A summary of the alignment counts can be found in /scratch/8793050.1.linga/tophat2/align_summary.txt
[2018-10-13 06:42:46] Run complete: 00:29:17 elapsed