[2018-10-13 15:33:45] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:33:45] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:33:45] Checking for Bowtie index files (genome)..
[2018-10-13 15:33:45] Checking for reference FASTA file
[2018-10-13 15:33:45] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:33:50] Reading known junctions from GTF file
[2018-10-13 15:33:58] Preparing reads
	 left reads: min. length=100, max. length=100, 502170 kept reads (280 discarded)
	right reads: min. length=100, max. length=100, 501827 kept reads (623 discarded)
[2018-10-13 15:34:30] Building transcriptome data files /scratch/8793324.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:34:55] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:46:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:47:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:47:48] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:47:48] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:48:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:48:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:48:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:49:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:49:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:49:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:50:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:50:15] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:50:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:50:39] Searching for junctions via segment mapping
[2018-10-13 15:55:02] Retrieving sequences for splices
[2018-10-13 15:58:42] Indexing splices
[2018-10-13 15:59:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:59:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:59:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:59:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:59:33] Joining segment hits
[2018-10-13 16:04:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:04:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:04:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:04:27] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:04:32] Joining segment hits
[2018-10-13 16:07:01] Reporting output tracks
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[2018-10-13 16:14:35] A summary of the alignment counts can be found in /scratch/8793324.1.linga/tophat2/align_summary.txt
[2018-10-13 16:14:35] Run complete: 00:40:50 elapsed