[2018-10-13 14:46:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:46:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:46:32] Checking for Bowtie index files (genome)..
[2018-10-13 14:46:32] Checking for reference FASTA file
[2018-10-13 14:46:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:46:35] Reading known junctions from GTF file
[2018-10-13 14:46:39] Preparing reads
	 left reads: min. length=100, max. length=100, 1175178 kept reads (166 discarded)
	right reads: min. length=100, max. length=100, 1174778 kept reads (566 discarded)
[2018-10-13 14:47:27] Building transcriptome data files /scratch/8793302.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:47:45] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:55:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:56:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:57:04] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:57:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:57:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:57:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:58:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:58:19] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:58:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:59:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:59:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:59:35] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:59:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:59:57] Searching for junctions via segment mapping
[2018-10-13 15:03:48] Retrieving sequences for splices
[2018-10-13 15:05:52] Indexing splices
[2018-10-13 15:06:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:06:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:06:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:06:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:06:36] Joining segment hits
[2018-10-13 15:09:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:09:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:09:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:09:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:09:28] Joining segment hits
[2018-10-13 15:11:53] Reporting output tracks
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[2018-10-13 15:20:53] A summary of the alignment counts can be found in /scratch/8793302.1.linga/tophat2/align_summary.txt
[2018-10-13 15:20:53] Run complete: 00:34:21 elapsed