[2018-10-13 12:10:58] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:10:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:10:58] Checking for Bowtie index files (genome)..
[2018-10-13 12:10:58] Checking for reference FASTA file
[2018-10-13 12:10:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:11:00] Reading known junctions from GTF file
[2018-10-13 12:11:02] Preparing reads
	 left reads: min. length=100, max. length=100, 1051071 kept reads (195 discarded)
	right reads: min. length=100, max. length=100, 1050830 kept reads (436 discarded)
[2018-10-13 12:11:31] Building transcriptome data files /scratch/8793228.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:11:45] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:17:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:17:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:18:55] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:18:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:19:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:19:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:19:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:19:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:19:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:20:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:20:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:20:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:20:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:21:05] Searching for junctions via segment mapping
[2018-10-13 12:26:24] Retrieving sequences for splices
[2018-10-13 12:27:36] Indexing splices
[2018-10-13 12:27:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:27:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:28:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:28:08] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:28:13] Joining segment hits
[2018-10-13 12:29:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:29:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:29:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:29:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:29:59] Joining segment hits
[2018-10-13 12:31:23] Reporting output tracks
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[2018-10-13 12:43:25] A summary of the alignment counts can be found in /scratch/8793228.1.c/tophat2/align_summary.txt
[2018-10-13 12:43:25] Run complete: 00:32:26 elapsed