[2017-08-30 13:58:53] Beginning TopHat run (v2.1.1)
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[2017-08-30 13:58:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-08-30 13:58:53] Checking for Bowtie index files (genome)..
[2017-08-30 13:58:53] Checking for reference FASTA file
[2017-08-30 13:58:53] Generating SAM header for Bowtie2Index/genome
[2017-08-30 13:58:55] Reading known junctions from GTF file
[2017-08-30 13:58:57] 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 14:08:31] Building transcriptome data files /scratch/469155.1.c/tophat2/tmp/RefSeq_GeneBody
[2017-08-30 14:08:41] Building Bowtie index from RefSeq_GeneBody.fa
[2017-08-30 14:14:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:18:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-08-30 14:23:21] Resuming TopHat pipeline with unmapped reads
[2017-08-30 14:23:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:32:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:32:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:33:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-08-30 14:42:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2017-08-30 14:43:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2017-08-30 14:44:01] Searching for junctions via segment mapping
[2017-08-30 14:46:10] Retrieving sequences for splices
[2017-08-30 14:47:22] Indexing splices
Building a SMALL index
[2017-08-30 14:47:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:47:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:47:50] Joining segment hits
[2017-08-30 14:49:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2017-08-30 14:49:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2017-08-30 14:49:36] Joining segment hits
[2017-08-30 14:51:07] Reporting output tracks
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[2017-08-30 15:08:01] A summary of the alignment counts can be found in /scratch/469155.1.c/tophat2/align_summary.txt
[2017-08-30 15:08:01] Run complete: 01:09:08 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 19 files...