[2018-10-13 16:14:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:14:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:14:34] Checking for Bowtie index files (genome)..
[2018-10-13 16:14:34] Checking for reference FASTA file
[2018-10-13 16:14:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:14:38] Reading known junctions from GTF file
[2018-10-13 16:14:43] Preparing reads
	 left reads: min. length=100, max. length=100, 231670 kept reads (159 discarded)
	right reads: min. length=100, max. length=100, 231432 kept reads (397 discarded)
[2018-10-13 16:14:53] Building transcriptome data files /scratch/8793348.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:15:13] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:22:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:23:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:23:48] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:23:49] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:24:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:24:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:24:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:24:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:24:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:25:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:25:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:25:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:25:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:25:58] Searching for junctions via segment mapping
[2018-10-13 16:28:40] Retrieving sequences for splices
[2018-10-13 16:30:51] Indexing splices
[2018-10-13 16:31:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:31:15] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:31:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:31:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:31:28] Joining segment hits
[2018-10-13 16:33:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:33:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:34:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:34:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:34:11] Joining segment hits
[2018-10-13 16:36:48] Reporting output tracks
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[2018-10-13 16:39:59] A summary of the alignment counts can be found in /scratch/8793348.1.linga/tophat2/align_summary.txt
[2018-10-13 16:39:59] Run complete: 00:25:24 elapsed