[2018-10-12 21:21:04] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:21:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:21:04] Checking for Bowtie index files (genome)..
[2018-10-12 21:21:04] Checking for reference FASTA file
[2018-10-12 21:21:04] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:21:06] Reading known junctions from GTF file
[2018-10-12 21:21:08] Preparing reads
	 left reads: min. length=100, max. length=100, 275707 kept reads (120 discarded)
	right reads: min. length=100, max. length=100, 275471 kept reads (356 discarded)
[2018-10-12 21:21:16] Building transcriptome data files /scratch/8792749.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:21:26] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:26:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:26:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:26:43] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:26:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:26:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:27:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:27:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:27:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:27:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:27:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:27:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:27:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:27:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:27:48] Searching for junctions via segment mapping
[2018-10-12 21:29:04] Retrieving sequences for splices
[2018-10-12 21:30:11] Indexing splices
[2018-10-12 21:30:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:30:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:30:26] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:30:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:30:31] Joining segment hits
[2018-10-12 21:31:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:31:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:31:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:31:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:31:49] Joining segment hits
[2018-10-12 21:32:58] Reporting output tracks
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[2018-10-12 21:34:31] A summary of the alignment counts can be found in /scratch/8792749.1.p8/tophat2/align_summary.txt
[2018-10-12 21:34:31] Run complete: 00:13:27 elapsed