[2018-10-12 23:06:48] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:06:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:06:48] Checking for Bowtie index files (genome)..
[2018-10-12 23:06:48] Checking for reference FASTA file
[2018-10-12 23:06:48] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:06:53] Reading known junctions from GTF file
[2018-10-12 23:06:57] Preparing reads
	 left reads: min. length=100, max. length=100, 393081 kept reads (220 discarded)
	right reads: min. length=100, max. length=100, 392729 kept reads (572 discarded)
[2018-10-12 23:07:14] Building transcriptome data files /scratch/8792824.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:07:35] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:16:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:16:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:17:31] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:17:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:18:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:18:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:18:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:18:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:18:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:19:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:19:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:20:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:20:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:20:29] Searching for junctions via segment mapping
[2018-10-12 23:23:11] Retrieving sequences for splices
[2018-10-12 23:25:21] Indexing splices
[2018-10-12 23:25:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:25:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:25:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:25:55] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:26:00] Joining segment hits
[2018-10-12 23:28:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:28:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:28:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:28:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:28:45] Joining segment hits
[2018-10-12 23:31:16] Reporting output tracks
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[2018-10-12 23:34:50] A summary of the alignment counts can be found in /scratch/8792824.1.linga/tophat2/align_summary.txt
[2018-10-12 23:34:50] Run complete: 00:28:02 elapsed