[2019-06-26 08:38:14] Beginning TopHat run (v2.1.1)
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[2019-06-26 08:38:14] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 08:38:14] Checking for Bowtie index files (genome)..
[2019-06-26 08:38:14] Checking for reference FASTA file
[2019-06-26 08:38:14] Generating SAM header for Bowtie2Index/genome
[2019-06-26 08:38:19] Reading known junctions from GTF file
[2019-06-26 08:38:23] Preparing reads
	 left reads: min. length=51, max. length=51, 20338864 kept reads (48011 discarded)
	right reads: min. length=51, max. length=51, 20373567 kept reads (13308 discarded)
[2019-06-26 08:50:00] Building transcriptome data files /scratch/7076159.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 08:50:19] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 08:57:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 09:09:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 09:20:25] Resuming TopHat pipeline with unmapped reads
[2019-06-26 09:20:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 09:30:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 09:31:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 09:33:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 09:41:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 09:42:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 09:43:46] Searching for junctions via segment mapping
[2019-06-26 09:49:21] Retrieving sequences for splices
[2019-06-26 09:51:51] Indexing splices
[2019-06-26 09:52:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 09:52:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 09:52:28] Joining segment hits
[2019-06-26 09:55:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 09:55:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 09:55:56] Joining segment hits
[2019-06-26 09:59:03] Reporting output tracks
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[2019-06-26 13:48:57] A summary of the alignment counts can be found in /scratch/7076159.1.linga/tophat2/align_summary.txt
[2019-06-26 13:48:57] Run complete: 05:10:42 elapsed