[2018-10-13 14:34:37] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:34:37] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:34:37] Checking for Bowtie index files (genome)..
[2018-10-13 14:34:37] Checking for reference FASTA file
[2018-10-13 14:34:37] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:34:41] Reading known junctions from GTF file
[2018-10-13 14:34:45] Preparing reads
	 left reads: min. length=100, max. length=100, 1458013 kept reads (193 discarded)
	right reads: min. length=100, max. length=100, 1457721 kept reads (485 discarded)
[2018-10-13 14:35:43] Building transcriptome data files /scratch/8793296.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:36:02] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:43:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:46:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:48:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:48:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:49:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:49:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:49:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:49:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:50:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:51:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:51:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:51:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:51:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:52:03] Searching for junctions via segment mapping
[2018-10-13 14:59:36] Retrieving sequences for splices
[2018-10-13 15:01:48] Indexing splices
[2018-10-13 15:02:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:02:20] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:02:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:02:44] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:02:55] Joining segment hits
[2018-10-13 15:05:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:05:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:05:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:06:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:06:18] Joining segment hits
[2018-10-13 15:08:58] Reporting output tracks
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[2018-10-13 15:42:01] A summary of the alignment counts can be found in /scratch/8793296.1.linga/tophat2/align_summary.txt
[2018-10-13 15:42:01] Run complete: 01:07:24 elapsed