[2017-08-30 15:51:27] Beginning TopHat run (v2.1.1)
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[2017-08-30 15:51:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-08-30 15:51:27] Checking for Bowtie index files (genome)..
[2017-08-30 15:51:27] Checking for reference FASTA file
[2017-08-30 15:51:27] Generating SAM header for Bowtie2Index/genome
[2017-08-30 15:51:29] Reading known junctions from GTF file
[2017-08-30 15:51:31] 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 16:00:50] Building transcriptome data files /scratch/469160.1.c/tophat2/tmp/RefSeq_GeneBody
[2017-08-30 16:01:00] Building Bowtie index from RefSeq_GeneBody.fa
[2017-08-30 16:06:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 16:10:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 16:15:16] Resuming TopHat pipeline with unmapped reads
[2017-08-30 16:15:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 16:23:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 16:24:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 16:25:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 16:33:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 16:34:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 16:35:25] Searching for junctions via segment mapping
[2017-08-30 16:37:35] Retrieving sequences for splices
[2017-08-30 16:38:47] Indexing splices
Building a SMALL index
[2017-08-30 16:39:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 16:39:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 16:39:29] Joining segment hits
[2017-08-30 16:41:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 16:41:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 16:41:21] Joining segment hits
[2017-08-30 16:42:51] Reporting output tracks
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[2017-08-30 16:59:58] A summary of the alignment counts can be found in /scratch/469160.1.c/tophat2/align_summary.txt
[2017-08-30 16:59:58] Run complete: 01:08:31 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 17 files...