[2017-08-30 15:10:29] Beginning TopHat run (v2.1.1)
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[2017-08-30 15:10:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-08-30 15:10:29] Checking for Bowtie index files (genome)..
[2017-08-30 15:10:29] Checking for reference FASTA file
[2017-08-30 15:10:29] Generating SAM header for Bowtie2Index/genome
[2017-08-30 15:10:31] Reading known junctions from GTF file
[2017-08-30 15:10:33] Preparing reads
	 left reads: min. length=50, max. length=50, 26516843 kept reads (1988 discarded)
	right reads: min. length=50, max. length=50, 26432385 kept reads (86446 discarded)
[2017-08-30 15:19:48] Building transcriptome data files /scratch/469156.1.p16/tophat2/tmp/RefSeq_GeneBody
[2017-08-30 15:19:57] Building Bowtie index from RefSeq_GeneBody.fa
[2017-08-30 15:24:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 15:29:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 15:33:29] Resuming TopHat pipeline with unmapped reads
[2017-08-30 15:33:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 15:41:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 15:42:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 15:43:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 15:51:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 15:51:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 15:52:40] Searching for junctions via segment mapping
[2017-08-30 15:54:41] Retrieving sequences for splices
[2017-08-30 15:55:47] Indexing splices
Building a SMALL index
[2017-08-30 15:55:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 15:56:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 15:56:10] Joining segment hits
[2017-08-30 15:57:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 15:57:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 15:57:48] Joining segment hits
[2017-08-30 15:59:15] Reporting output tracks
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[2017-08-30 16:15:11] A summary of the alignment counts can be found in /scratch/469156.1.p16/tophat2/align_summary.txt
[2017-08-30 16:15:11] Run complete: 01:04:42 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 19 files...