[2018-10-13 02:07:25] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:07:25] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:07:25] Checking for Bowtie index files (genome)..
[2018-10-13 02:07:25] Checking for reference FASTA file
[2018-10-13 02:07:25] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:07:30] Reading known junctions from GTF file
[2018-10-13 02:07:35] Preparing reads
	 left reads: min. length=100, max. length=100, 264726 kept reads (186 discarded)
	right reads: min. length=100, max. length=100, 264367 kept reads (545 discarded)
[2018-10-13 02:07:46] Building transcriptome data files /scratch/8792907.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:08:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:16:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:17:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:17:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:17:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:18:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:18:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:18:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:18:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:18:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:19:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:19:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:19:44] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:19:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:20:04] Searching for junctions via segment mapping
[2018-10-13 02:22:37] Retrieving sequences for splices
[2018-10-13 02:24:46] Indexing splices
[2018-10-13 02:25:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:25:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:25:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:25:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:25:21] Joining segment hits
[2018-10-13 02:27:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:27:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:27:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:27:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:27:53] Joining segment hits
[2018-10-13 02:30:29] Reporting output tracks
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[2018-10-13 02:33:39] A summary of the alignment counts can be found in /scratch/8792907.1.linga/tophat2/align_summary.txt
[2018-10-13 02:33:39] Run complete: 00:26:13 elapsed