[2017-08-30 13:54:45] Beginning TopHat run (v2.1.1)
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[2017-08-30 13:54:45] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-08-30 13:54:45] Checking for Bowtie index files (genome)..
[2017-08-30 13:54:45] Checking for reference FASTA file
[2017-08-30 13:54:45] Generating SAM header for Bowtie2Index/genome
[2017-08-30 13:54:47] Reading known junctions from GTF file
[2017-08-30 13:54:49] Preparing reads
	 left reads: min. length=50, max. length=50, 19791046 kept reads (1529 discarded)
	right reads: min. length=50, max. length=50, 19728925 kept reads (63650 discarded)
[2017-08-30 14:01:44] Building transcriptome data files /scratch/469152.1.p16/tophat2/tmp/RefSeq_GeneBody
[2017-08-30 14:01:52] Building Bowtie index from RefSeq_GeneBody.fa
[2017-08-30 14:06:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:10:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:13:25] Resuming TopHat pipeline with unmapped reads
[2017-08-30 14:13:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:19:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:20:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:21:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:27:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:28:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:29:17] Searching for junctions via segment mapping
[2017-08-30 14:31:12] Retrieving sequences for splices
[2017-08-30 14:32:18] Indexing splices
Building a SMALL index
[2017-08-30 14:32:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:32:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:32:47] Joining segment hits
[2017-08-30 14:34:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:34:20] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:34:30] Joining segment hits
[2017-08-30 14:35:54] Reporting output tracks
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[2017-08-30 14:48:00] A summary of the alignment counts can be found in /scratch/469152.1.p16/tophat2/align_summary.txt
[2017-08-30 14:48:00] Run complete: 00:53:14 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 12 files...