[2018-10-13 07:03:45] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:03:45] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:03:45] Checking for Bowtie index files (genome)..
[2018-10-13 07:03:45] Checking for reference FASTA file
[2018-10-13 07:03:45] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:03:50] Reading known junctions from GTF file
[2018-10-13 07:03:54] Preparing reads
	 left reads: min. length=100, max. length=100, 665757 kept reads (51 discarded)
	right reads: min. length=100, max. length=100, 665667 kept reads (141 discarded)
[2018-10-13 07:04:24] Building transcriptome data files /scratch/8793074.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:04:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:12:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:13:40] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:14:37] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:14:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:15:05] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:15:14] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:15:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:15:36] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:15:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:16:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:16:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:16:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:16:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:17:00] Searching for junctions via segment mapping
[2018-10-13 07:22:12] Retrieving sequences for splices
[2018-10-13 07:24:30] Indexing splices
[2018-10-13 07:24:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:24:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:25:03] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:25:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:25:18] Joining segment hits
[2018-10-13 07:27:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:27:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:27:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:27:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:27:59] Joining segment hits
[2018-10-13 07:30:28] Reporting output tracks
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[2018-10-13 07:40:53] A summary of the alignment counts can be found in /scratch/8793074.1.linga/tophat2/align_summary.txt
[2018-10-13 07:40:53] Run complete: 00:37:07 elapsed