[2019-06-26 11:47:08] Beginning TopHat run (v2.1.1)
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[2019-06-26 11:47:08] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 11:47:08] Checking for Bowtie index files (genome)..
[2019-06-26 11:47:08] Checking for reference FASTA file
[2019-06-26 11:47:08] Generating SAM header for Bowtie2Index/genome
[2019-06-26 11:47:13] Reading known junctions from GTF file
[2019-06-26 11:47:17] Preparing reads
	 left reads: min. length=51, max. length=51, 22206308 kept reads (106233 discarded)
	right reads: min. length=51, max. length=51, 22276084 kept reads (36457 discarded)
[2019-06-26 11:59:23] Building transcriptome data files /scratch/7076162.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 11:59:43] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 12:06:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 12:19:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 12:31:23] Resuming TopHat pipeline with unmapped reads
[2019-06-26 12:31:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 12:46:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 12:49:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 12:51:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 13:01:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 13:02:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 13:03:47] Searching for junctions via segment mapping
[2019-06-26 13:10:40] Retrieving sequences for splices
[2019-06-26 13:13:46] Indexing splices
[2019-06-26 13:14:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 13:14:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 13:14:38] Joining segment hits
[2019-06-26 13:18:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 13:18:57] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 13:19:11] Joining segment hits
[2019-06-26 13:22:59] Reporting output tracks
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[2019-06-26 15:29:22] A summary of the alignment counts can be found in /scratch/7076162.1.linga/tophat2/align_summary.txt
[2019-06-26 15:29:22] Run complete: 03:42:14 elapsed