[2019-04-25 22:43:23] Beginning TopHat run (v2.1.1)
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[2019-04-25 22:43:23] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-25 22:43:23] Checking for Bowtie index files (genome)..
[2019-04-25 22:43:23] Checking for reference FASTA file
[2019-04-25 22:43:23] Generating SAM header for Bowtie2Index/genome
[2019-04-25 22:43:26] Reading known junctions from GTF file
[2019-04-25 22:43:36] Preparing reads
	 left reads: min. length=50, max. length=50, 43236129 kept reads (15093 discarded)
	right reads: min. length=50, max. length=50, 43164734 kept reads (86488 discarded)
[2019-04-25 22:55:35] Building transcriptome data files /scratch/5574194.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-04-25 22:55:45] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-25 23:01:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-25 23:12:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-25 23:23:57] Resuming TopHat pipeline with unmapped reads
[2019-04-25 23:23:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-25 23:28:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-25 23:28:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-25 23:29:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-25 23:33:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-25 23:34:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-25 23:34:51] Searching for junctions via segment mapping
[2019-04-25 23:37:21] Retrieving sequences for splices
[2019-04-25 23:38:26] Indexing splices
[2019-04-25 23:38:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-25 23:38:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-25 23:39:06] Joining segment hits
[2019-04-25 23:40:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-25 23:40:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-25 23:40:55] Joining segment hits
[2019-04-25 23:42:20] Reporting output tracks
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[2019-04-26 00:13:34] A summary of the alignment counts can be found in /scratch/5574194.1.c/tophat2/align_summary.txt
[2019-04-26 00:13:34] Run complete: 01:30:10 elapsed