[2018-10-13 18:35:16] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 18:35:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:35:16] Checking for Bowtie index files (genome)..
[2018-10-13 18:35:16] Checking for reference FASTA file
[2018-10-13 18:35:16] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:35:18] Reading known junctions from GTF file
[2018-10-13 18:35:21] Preparing reads
	 left reads: min. length=100, max. length=100, 322962 kept reads (172 discarded)
	right reads: min. length=100, max. length=100, 322736 kept reads (398 discarded)
[2018-10-13 18:35:29] Building transcriptome data files /scratch/8793445.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:35:39] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:40:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:40:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:40:54] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:40:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:41:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:41:12] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:41:17] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:41:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:41:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:41:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:41:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:41:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:41:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:41:58] Searching for junctions via segment mapping
[2018-10-13 18:43:17] Retrieving sequences for splices
[2018-10-13 18:44:24] Indexing splices
[2018-10-13 18:44:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:44:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:44:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:44:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:44:43] Joining segment hits
[2018-10-13 18:45:52] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:45:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:45:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:45:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:46:02] Joining segment hits
[2018-10-13 18:47:11] Reporting output tracks
-----------------------------------------------
[2018-10-13 18:48:45] A summary of the alignment counts can be found in /scratch/8793445.1.p16/tophat2/align_summary.txt
[2018-10-13 18:48:45] Run complete: 00:13:29 elapsed