[2018-10-13 14:30:23] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:30:23] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:30:23] Checking for Bowtie index files (genome)..
[2018-10-13 14:30:23] Checking for reference FASTA file
[2018-10-13 14:30:23] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:30:28] Reading known junctions from GTF file
[2018-10-13 14:30:32] Preparing reads
	 left reads: min. length=100, max. length=100, 760053 kept reads (38 discarded)
	right reads: min. length=100, max. length=100, 759823 kept reads (268 discarded)
[2018-10-13 14:31:02] Building transcriptome data files /scratch/8793292.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:31:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:38:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:39:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:40:08] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:40:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:40:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:40:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:40:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:41:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:41:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:41:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:41:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:41:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:42:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:42:18] Searching for junctions via segment mapping
[2018-10-13 14:45:59] Retrieving sequences for splices
[2018-10-13 14:47:58] Indexing splices
[2018-10-13 14:48:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:48:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:48:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:48:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:48:41] Joining segment hits
[2018-10-13 14:50:56] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:51:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:51:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:51:12] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:51:17] Joining segment hits
[2018-10-13 14:53:33] Reporting output tracks
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[2018-10-13 15:02:14] A summary of the alignment counts can be found in /scratch/8793292.1.linga/tophat2/align_summary.txt
[2018-10-13 15:02:14] Run complete: 00:31:50 elapsed