[2019-07-17 22:17:11] Beginning TopHat run (v2.1.1)
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[2019-07-17 22:17:11] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 22:17:13] Checking for Bowtie index files (genome)..
[2019-07-17 22:17:13] Checking for reference FASTA file
[2019-07-17 22:17:13] Generating SAM header for Bowtie2Index/genome
[2019-07-17 22:17:18] Reading known junctions from GTF file
[2019-07-17 22:17:22] Preparing reads
	 left reads: min. length=51, max. length=51, 18516200 kept reads (43568 discarded)
	right reads: min. length=51, max. length=51, 18546207 kept reads (13561 discarded)
[2019-07-17 22:28:13] Building transcriptome data files /scratch/7776691.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 22:28:30] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 22:35:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 22:43:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 22:51:17] Resuming TopHat pipeline with unmapped reads
[2019-07-17 22:51:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 22:59:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-07-17 23:00:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-07-17 23:01:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 23:08:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-07-17 23:09:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-07-17 23:10:34] Searching for junctions via segment mapping
[2019-07-17 23:15:17] Retrieving sequences for splices
[2019-07-17 23:17:45] Indexing splices
[2019-07-17 23:18:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-07-17 23:18:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-07-17 23:18:24] Joining segment hits
[2019-07-17 23:21:26] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-07-17 23:21:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-07-17 23:21:46] Joining segment hits
[2019-07-17 23:24:39] Reporting output tracks
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[2019-07-18 01:25:19] A summary of the alignment counts can be found in /scratch/7776691.1.linga/tophat2/align_summary.txt
[2019-07-18 01:25:19] Run complete: 03:08:08 elapsed