[2018-12-04 13:43:33] Beginning TopHat run (v2.1.1)
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[2018-12-04 13:43:33] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-12-04 13:43:33] Checking for Bowtie index files (genome)..
[2018-12-04 13:43:33] Checking for reference FASTA file
[2018-12-04 13:43:33] Generating SAM header for Bowtie2Index/genome
[2018-12-04 13:43:38] Reading known junctions from GTF file
[2018-12-04 13:43:44] Preparing reads
	 left reads: min. length=50, max. length=50, 46541849 kept reads (27502 discarded)
	right reads: min. length=50, max. length=50, 46475319 kept reads (94032 discarded)
[2018-12-04 14:04:57] Building transcriptome data files /scratch/9977263.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-12-04 14:05:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-12-04 14:14:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-12-04 14:38:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-12-04 15:01:43] Resuming TopHat pipeline with unmapped reads
[2018-12-04 15:01:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-12-04 15:11:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2018-12-04 15:13:14] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2018-12-04 15:14:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-12-04 15:24:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2018-12-04 15:26:22] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2018-12-04 15:28:26] Searching for junctions via segment mapping
[2018-12-04 15:33:20] Retrieving sequences for splices
[2018-12-04 15:35:59] Indexing splices
[2018-12-04 15:36:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2018-12-04 15:36:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2018-12-04 15:37:09] Joining segment hits
[2018-12-04 15:40:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2018-12-04 15:40:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2018-12-04 15:41:07] Joining segment hits
[2018-12-04 15:44:20] Reporting output tracks
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[2018-12-04 16:22:27] A summary of the alignment counts can be found in /scratch/9977263.1.linga/tophat2/align_summary.txt
[2018-12-04 16:22:27] Run complete: 02:38:54 elapsed