[2018-10-13 14:20:30] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:20:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:20:30] Checking for Bowtie index files (genome)..
[2018-10-13 14:20:30] Checking for reference FASTA file
[2018-10-13 14:20:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:20:34] Reading known junctions from GTF file
[2018-10-13 14:20:38] Preparing reads
	 left reads: min. length=100, max. length=100, 2875507 kept reads (576 discarded)
	right reads: min. length=100, max. length=100, 2874861 kept reads (1222 discarded)
[2018-10-13 14:22:23] Building transcriptome data files /scratch/8793287.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:22:41] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:30:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:38:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:46:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:46:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:47:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:48:26] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:49:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:50:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:50:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:52:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:53:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:54:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:54:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:55:44] Searching for junctions via segment mapping
[2018-10-13 15:21:06] Retrieving sequences for splices
[2018-10-13 15:23:07] Indexing splices
[2018-10-13 15:23:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:24:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:24:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:25:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:26:31] Joining segment hits
[2018-10-13 15:29:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:29:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:30:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:31:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:32:33] Joining segment hits
[2018-10-13 15:35:47] Reporting output tracks
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[2018-10-13 17:49:16] A summary of the alignment counts can be found in /scratch/8793287.1.linga/tophat2/align_summary.txt
[2018-10-13 17:49:16] Run complete: 03:28:46 elapsed