[2019-06-26 12:19:21] Beginning TopHat run (v2.1.1)
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[2019-06-26 12:19:21] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 12:19:22] Checking for Bowtie index files (genome)..
[2019-06-26 12:19:22] Checking for reference FASTA file
[2019-06-26 12:19:22] Generating SAM header for Bowtie2Index/genome
[2019-06-26 12:19:23] Reading known junctions from GTF file
[2019-06-26 12:19:25] Preparing reads
	 left reads: min. length=51, max. length=51, 21992883 kept reads (57240 discarded)
	right reads: min. length=51, max. length=51, 22033349 kept reads (16774 discarded)
[2019-06-26 12:26:15] Building transcriptome data files /scratch/7076163.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 12:26:24] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 12:30:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 12:37:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 12:44:21] Resuming TopHat pipeline with unmapped reads
[2019-06-26 12:44:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 12:50:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 12:50:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 12:51:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 12:56:07] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 12:56:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 12:57:17] Searching for junctions via segment mapping
[2019-06-26 12:59:20] Retrieving sequences for splices
[2019-06-26 13:00:28] Indexing splices
[2019-06-26 13:00:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 13:00:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 13:00:48] Joining segment hits
[2019-06-26 13:02:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 13:02:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 13:02:27] Joining segment hits
[2019-06-26 13:03:47] Reporting output tracks
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[2019-06-26 14:28:02] A summary of the alignment counts can be found in /scratch/7076163.1.p8/tophat2/align_summary.txt
[2019-06-26 14:28:02] Run complete: 02:08:40 elapsed