[2018-10-13 15:50:05] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:50:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:50:05] Checking for Bowtie index files (genome)..
[2018-10-13 15:50:05] Checking for reference FASTA file
[2018-10-13 15:50:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:50:07] Reading known junctions from GTF file
[2018-10-13 15:50:09] Preparing reads
	 left reads: min. length=100, max. length=100, 214734 kept reads (96 discarded)
	right reads: min. length=100, max. length=100, 214635 kept reads (195 discarded)
[2018-10-13 15:50:16] Building transcriptome data files /scratch/8793330.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:50:26] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:56:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:56:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:56:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:56:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:56:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:56:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:57:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:57:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:57:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:57:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:57:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:57:28] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:57:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:57:36] Searching for junctions via segment mapping
[2018-10-13 15:59:13] Retrieving sequences for splices
[2018-10-13 16:00:26] Indexing splices
[2018-10-13 16:00:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:00:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:00:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:00:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:00:47] Joining segment hits
[2018-10-13 16:02:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:02:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:02:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:02:14] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:02:16] Joining segment hits
[2018-10-13 16:03:35] Reporting output tracks
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[2018-10-13 16:05:41] A summary of the alignment counts can be found in /scratch/8793330.1.c/tophat2/align_summary.txt
[2018-10-13 16:05:41] Run complete: 00:15:36 elapsed