[2019-06-26 16:42:36] Beginning TopHat run (v2.1.1)
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[2019-06-26 16:42:36] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 16:42:36] Checking for Bowtie index files (genome)..
[2019-06-26 16:42:40] Checking for reference FASTA file
[2019-06-26 16:42:40] Generating SAM header for Bowtie2Index/genome
[2019-06-26 16:42:41] Reading known junctions from GTF file
[2019-06-26 16:42:43] Preparing reads
	 left reads: min. length=35, max. length=76, 24075361 kept reads (618622 discarded)
	right reads: min. length=35, max. length=76, 24574715 kept reads (119268 discarded)
[2019-06-26 16:51:59] Building transcriptome data files /scratch/7076176.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 16:52:08] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 16:56:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 17:06:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 17:17:57] Resuming TopHat pipeline with unmapped reads
[2019-06-26 17:17:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 17:22:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 17:23:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 17:24:33] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 17:25:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 17:31:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 17:33:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 17:35:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 17:37:33] Searching for junctions via segment mapping
[2019-06-26 17:41:15] Retrieving sequences for splices
[2019-06-26 17:42:23] Indexing splices
[2019-06-26 17:42:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 17:42:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 17:43:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 17:43:41] Joining segment hits
[2019-06-26 17:45:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 17:45:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 17:46:10] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 17:47:05] Joining segment hits
[2019-06-26 17:48:57] Reporting output tracks
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[2019-06-26 19:17:01] A summary of the alignment counts can be found in /scratch/7076176.1.p16/tophat2/align_summary.txt
[2019-06-26 19:17:01] Run complete: 02:34:24 elapsed