[2018-12-18 14:30:27] Beginning TopHat run (v2.1.1)
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[2018-12-18 14:30:27] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2018-12-18 14:30:27] Checking for Bowtie index files (genome)..
[2018-12-18 14:30:27] Checking for reference FASTA file
[2018-12-18 14:30:27] Generating SAM header for Bowtie2Index/genome
[2018-12-18 14:30:32] Reading known junctions from GTF file
[2018-12-18 14:30:36] Preparing reads
	 left reads: min. length=50, max. length=50, 16517130 kept reads (9019 discarded)
	right reads: min. length=50, max. length=50, 16511865 kept reads (14284 discarded)
[2018-12-18 14:38:40] Building transcriptome data files /scratch/359397.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-12-18 14:38:57] Building Bowtie index from RefSeq_GeneBody.fa
[2018-12-18 14:46:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-12-18 14:57:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-12-18 15:08:48] Resuming TopHat pipeline with unmapped reads
[2018-12-18 15:08:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-12-18 15:18:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2018-12-18 15:19:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2018-12-18 15:20:47] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-12-18 15:30:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2018-12-18 15:31:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2018-12-18 15:33:22] Searching for junctions via segment mapping
[2018-12-18 15:37:50] Retrieving sequences for splices
[2018-12-18 15:39:54] Indexing splices
Building a SMALL index
[2018-12-18 15:40:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2018-12-18 15:40:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2018-12-18 15:40:41] Joining segment hits
[2018-12-18 15:43:23] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2018-12-18 15:43:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2018-12-18 15:43:47] Joining segment hits
[2018-12-18 15:46:27] Reporting output tracks
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[2018-12-18 16:25:38] A summary of the alignment counts can be found in /scratch/359397.1.linga/tophat2/align_summary.txt
[2018-12-18 16:25:38] Run complete: 01:55:11 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 12 files...