[2018-12-04 15:01:02] Beginning TopHat run (v2.1.1)
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[2018-12-04 15:01:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-12-04 15:01:02] Checking for Bowtie index files (genome)..
[2018-12-04 15:01:02] Checking for reference FASTA file
[2018-12-04 15:01:02] Generating SAM header for Bowtie2Index/genome
[2018-12-04 15:01:08] Reading known junctions from GTF file
[2018-12-04 15:01:15] Preparing reads
	 left reads: min. length=50, max. length=50, 43236129 kept reads (15093 discarded)
	right reads: min. length=50, max. length=50, 43164734 kept reads (86488 discarded)
[2018-12-04 15:22:48] Building transcriptome data files /scratch/9977299.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-12-04 15:23:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-12-04 15:32:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-12-04 16:13:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-12-04 16:55:06] Resuming TopHat pipeline with unmapped reads
[2018-12-04 16:55:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-12-04 17:04:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2018-12-04 17:06:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2018-12-04 17:07:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-12-04 17:17:07] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2018-12-04 17:18:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2018-12-04 17:20:12] Searching for junctions via segment mapping
[2018-12-04 17:25:37] Retrieving sequences for splices
[2018-12-04 17:27:47] Indexing splices
[2018-12-04 17:28:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2018-12-04 17:28:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2018-12-04 17:28:54] Joining segment hits
[2018-12-04 17:31:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2018-12-04 17:32:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2018-12-04 17:32:37] Joining segment hits
[2018-12-04 17:35:28] Reporting output tracks
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[2018-12-04 18:48:42] A summary of the alignment counts can be found in /scratch/9977299.1.linga/tophat2/align_summary.txt
[2018-12-04 18:48:42] Run complete: 03:47:39 elapsed