[2018-10-13 15:29:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:29:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:29:31] Checking for Bowtie index files (genome)..
[2018-10-13 15:29:31] Checking for reference FASTA file
[2018-10-13 15:29:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:29:36] Reading known junctions from GTF file
[2018-10-13 15:29:40] Preparing reads
	 left reads: min. length=100, max. length=100, 432653 kept reads (231 discarded)
	right reads: min. length=100, max. length=100, 432260 kept reads (624 discarded)
[2018-10-13 15:29:58] Building transcriptome data files /scratch/8793321.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:30:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:37:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:38:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:38:49] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:38:49] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:39:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:39:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:39:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:39:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:39:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:40:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:40:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:40:35] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:40:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:40:56] Searching for junctions via segment mapping
[2018-10-13 15:43:47] Retrieving sequences for splices
[2018-10-13 15:45:47] Indexing splices
[2018-10-13 15:46:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:46:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:46:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:46:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:46:24] Joining segment hits
[2018-10-13 15:48:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:48:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:48:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:48:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:49:04] Joining segment hits
[2018-10-13 15:51:38] Reporting output tracks
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[2018-10-13 15:55:43] A summary of the alignment counts can be found in /scratch/8793321.1.linga/tophat2/align_summary.txt
[2018-10-13 15:55:43] Run complete: 00:26:11 elapsed