[2019-06-18 11:07:57] Beginning TopHat run (v2.1.1)
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[2019-06-18 11:07:57] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-18 11:07:57] Checking for Bowtie index files (genome)..
[2019-06-18 11:07:57] Checking for reference FASTA file
[2019-06-18 11:07:57] Generating SAM header for Bowtie2Index/genome
[2019-06-18 11:08:03] Reading known junctions from GTF file
[2019-06-18 11:08:07] Preparing reads
	 left reads: min. length=50, max. length=50, 68322598 kept reads (117578 discarded)
	right reads: min. length=50, max. length=50, 68129352 kept reads (310824 discarded)
[2019-06-18 11:40:19] Building transcriptome data files /scratch/6794466.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-18 11:40:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-18 11:48:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 12:07:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 12:26:37] Resuming TopHat pipeline with unmapped reads
[2019-06-18 12:26:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 12:55:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 12:59:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 13:05:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 13:35:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 13:40:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 13:48:21] Searching for junctions via segment mapping
[2019-06-18 13:58:21] Retrieving sequences for splices
[2019-06-18 14:00:48] Indexing splices
[2019-06-18 14:01:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 14:01:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 14:02:38] Joining segment hits
[2019-06-18 14:06:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 14:07:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 14:08:47] Joining segment hits
[2019-06-18 14:13:13] Reporting output tracks
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[2019-06-18 15:19:45] A summary of the alignment counts can be found in /scratch/6794466.1.linga/tophat2/align_summary.txt
[2019-06-18 15:19:45] Run complete: 04:11:47 elapsed