[2017-08-30 13:55:32] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2017-08-30 13:55:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-08-30 13:55:33] Checking for Bowtie index files (genome)..
[2017-08-30 13:55:33] Checking for reference FASTA file
[2017-08-30 13:55:33] Generating SAM header for Bowtie2Index/genome
[2017-08-30 13:55:34] Reading known junctions from GTF file
[2017-08-30 13:55:37] 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 14:02:37] Building transcriptome data files /scratch/469151.1.p8/tophat2/tmp/RefSeq_GeneBody
[2017-08-30 14:02:45] Building Bowtie index from RefSeq_GeneBody.fa
[2017-08-30 14:07:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:10:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:14:18] Resuming TopHat pipeline with unmapped reads
[2017-08-30 14:14:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:20:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:21:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:22:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:28:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:29:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:30:12] Searching for junctions via segment mapping
[2017-08-30 14:32:06] Retrieving sequences for splices
[2017-08-30 14:33:12] Indexing splices
Building a SMALL index
[2017-08-30 14:33:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:33:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:33:42] Joining segment hits
[2017-08-30 14:35:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:35:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:35:25] Joining segment hits
[2017-08-30 14:36:47] Reporting output tracks
-----------------------------------------------
[2017-08-30 14:48:53] A summary of the alignment counts can be found in /scratch/469151.1.p8/tophat2/align_summary.txt
[2017-08-30 14:48:53] Run complete: 00:53:21 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 12 files...