[2017-08-30 15:43:02] Beginning TopHat run (v2.1.1)
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[2017-08-30 15:43:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-08-30 15:43:02] Checking for Bowtie index files (genome)..
[2017-08-30 15:43:02] Checking for reference FASTA file
[2017-08-30 15:43:02] Generating SAM header for Bowtie2Index/genome
[2017-08-30 15:43:04] Reading known junctions from GTF file
[2017-08-30 15:43:06] Preparing reads
	 left reads: min. length=50, max. length=50, 25871784 kept reads (1436 discarded)
	right reads: min. length=50, max. length=50, 25791817 kept reads (81403 discarded)
[2017-08-30 15:52:32] Building transcriptome data files /scratch/469159.1.c/tophat2/tmp/RefSeq_GeneBody
[2017-08-30 15:52:41] Building Bowtie index from RefSeq_GeneBody.fa
[2017-08-30 15:58:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 16:02:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 16:06:54] Resuming TopHat pipeline with unmapped reads
[2017-08-30 16:06:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 16:15:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 16:16:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 16:17:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 16:25:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 16:26:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 16:27:10] Searching for junctions via segment mapping
[2017-08-30 16:29:20] Retrieving sequences for splices
[2017-08-30 16:30:32] Indexing splices
Building a SMALL index
[2017-08-30 16:30:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 16:30:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 16:31:10] Joining segment hits
[2017-08-30 16:32:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 16:32:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 16:33:02] Joining segment hits
[2017-08-30 16:34:32] Reporting output tracks
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[2017-08-30 16:51:39] A summary of the alignment counts can be found in /scratch/469159.1.c/tophat2/align_summary.txt
[2017-08-30 16:51:39] Run complete: 01:08:37 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 17 files...