[2019-06-26 11:21:37] Beginning TopHat run (v2.1.1)
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[2019-06-26 11:21:37] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 11:21:37] Checking for Bowtie index files (genome)..
[2019-06-26 11:21:37] Checking for reference FASTA file
[2019-06-26 11:21:37] Generating SAM header for Bowtie2Index/genome
[2019-06-26 11:21:38] Reading known junctions from GTF file
[2019-06-26 11:21:40] Preparing reads
	 left reads: min. length=51, max. length=51, 17852522 kept reads (38231 discarded)
	right reads: min. length=51, max. length=51, 17880221 kept reads (10532 discarded)
[2019-06-26 11:27:13] Building transcriptome data files /scratch/7076161.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 11:27:22] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 11:31:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 11:38:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 11:43:29] Resuming TopHat pipeline with unmapped reads
[2019-06-26 11:43:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 11:48:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 11:48:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 11:49:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 11:53:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 11:53:50] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 11:54:22] Searching for junctions via segment mapping
[2019-06-26 11:56:17] Retrieving sequences for splices
[2019-06-26 11:57:25] Indexing splices
[2019-06-26 11:57:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 11:57:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 11:57:42] Joining segment hits
[2019-06-26 11:59:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 11:59:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 11:59:16] Joining segment hits
[2019-06-26 12:00:34] Reporting output tracks
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[2019-06-26 12:47:58] A summary of the alignment counts can be found in /scratch/7076161.1.p16/tophat2/align_summary.txt
[2019-06-26 12:47:58] Run complete: 01:26:21 elapsed