[2017-08-30 13:54:48] Beginning TopHat run (v2.1.1)
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[2017-08-30 13:54:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-08-30 13:54:49] Checking for Bowtie index files (genome)..
[2017-08-30 13:54:49] Checking for reference FASTA file
[2017-08-30 13:54:49] Generating SAM header for Bowtie2Index/genome
[2017-08-30 13:54:50] Reading known junctions from GTF file
[2017-08-30 13:54:53] Preparing reads
	 left reads: min. length=50, max. length=50, 26213002 kept reads (2438 discarded)
	right reads: min. length=50, max. length=50, 26126032 kept reads (89408 discarded)
[2017-08-30 14:03:51] Building transcriptome data files /scratch/469153.1.p16/tophat2/tmp/RefSeq_GeneBody
[2017-08-30 14:04:00] Building Bowtie index from RefSeq_GeneBody.fa
[2017-08-30 14:08:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:13:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:17:39] Resuming TopHat pipeline with unmapped reads
[2017-08-30 14:17:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:25:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:25:42] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:26:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:33:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:34:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:35:11] Searching for junctions via segment mapping
[2017-08-30 14:37:11] Retrieving sequences for splices
[2017-08-30 14:38:17] Indexing splices
Building a SMALL index
[2017-08-30 14:38:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:38:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:38:41] Joining segment hits
[2017-08-30 14:40:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:40:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:40:18] Joining segment hits
[2017-08-30 14:41:42] Reporting output tracks
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[2017-08-30 15:08:36] A summary of the alignment counts can be found in /scratch/469153.1.p16/tophat2/align_summary.txt
[2017-08-30 15:08:36] Run complete: 01:13:47 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 19 files...