[2019-04-25 19:39:37] Beginning TopHat run (v2.1.1)
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[2019-04-25 19:39:37] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-25 19:39:39] Checking for Bowtie index files (genome)..
[2019-04-25 19:39:39] Checking for reference FASTA file
[2019-04-25 19:39:39] Generating SAM header for Bowtie2Index/genome
[2019-04-25 19:39:45] Reading known junctions from GTF file
[2019-04-25 19:39:49] Preparing reads
	 left reads: min. length=50, max. length=50, 46541849 kept reads (27502 discarded)
	right reads: min. length=50, max. length=50, 46475319 kept reads (94032 discarded)
[2019-04-25 19:57:10] Building transcriptome data files /scratch/5574173.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-25 19:57:26] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-25 20:05:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-25 20:25:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-25 20:45:43] Resuming TopHat pipeline with unmapped reads
[2019-04-25 20:45:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-25 20:53:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-25 20:55:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-25 20:56:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-25 21:04:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-25 21:06:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-25 21:07:49] Searching for junctions via segment mapping
[2019-04-25 21:12:01] Retrieving sequences for splices
[2019-04-25 21:13:50] Indexing splices
[2019-04-25 21:14:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-25 21:14:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-25 21:14:54] Joining segment hits
[2019-04-25 21:17:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-25 21:17:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-25 21:18:10] Joining segment hits
[2019-04-25 21:20:40] Reporting output tracks
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[2019-04-25 21:49:35] A summary of the alignment counts can be found in /scratch/5574173.1.linga/tophat2/align_summary.txt
[2019-04-25 21:49:35] Run complete: 02:09:57 elapsed