[2019-06-18 11:07:40] Beginning TopHat run (v2.1.1)
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[2019-06-18 11:07:40] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-18 11:07:40] Checking for Bowtie index files (genome)..
[2019-06-18 11:07:40] Checking for reference FASTA file
[2019-06-18 11:07:40] Generating SAM header for Bowtie2Index/genome
[2019-06-18 11:07:48] Reading known junctions from GTF file
[2019-06-18 11:07:56] Preparing reads
	 left reads: min. length=50, max. length=50, 59283327 kept reads (65539 discarded)
	right reads: min. length=50, max. length=50, 59112845 kept reads (236021 discarded)
[2019-06-18 12:02:31] Building transcriptome data files /scratch/6794462.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-18 12:03:09] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-18 12:12:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 12:37:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 13:00:41] Resuming TopHat pipeline with unmapped reads
[2019-06-18 13:00:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 13:36:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 13:40:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 13:46:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 14:25:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 14:30:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 14:38:38] Searching for junctions via segment mapping
[2019-06-18 14:48:45] Retrieving sequences for splices
[2019-06-18 14:51:11] Indexing splices
[2019-06-18 14:51:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 14:52:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 14:53:21] Joining segment hits
[2019-06-18 14:58:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 14:59:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 15:00:18] Joining segment hits
[2019-06-18 15:06:24] Reporting output tracks
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[2019-06-18 16:40:16] A summary of the alignment counts can be found in /scratch/6794462.1.linga/tophat2/align_summary.txt
[2019-06-18 16:40:16] Run complete: 05:32:35 elapsed