[2018-10-13 10:20:02] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 10:20:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:20:02] Checking for Bowtie index files (genome)..
[2018-10-13 10:20:02] Checking for reference FASTA file
[2018-10-13 10:20:02] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:20:07] Reading known junctions from GTF file
[2018-10-13 10:20:11] Preparing reads
	 left reads: min. length=100, max. length=100, 1689880 kept reads (129 discarded)
	right reads: min. length=100, max. length=100, 1689356 kept reads (653 discarded)
[2018-10-13 10:21:22] Building transcriptome data files /scratch/8793171.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:21:41] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:29:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:30:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:32:17] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:32:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:33:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:33:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:33:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:33:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:34:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:34:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:35:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:35:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:35:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:35:54] Searching for junctions via segment mapping
[2018-10-13 10:40:40] Retrieving sequences for splices
[2018-10-13 10:42:42] Indexing splices
[2018-10-13 10:43:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:43:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:43:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:43:27] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:43:34] Joining segment hits
[2018-10-13 10:46:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:46:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:46:33] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:46:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:46:49] Joining segment hits
[2018-10-13 10:49:25] Reporting output tracks
-----------------------------------------------
[2018-10-13 11:05:12] A summary of the alignment counts can be found in /scratch/8793171.1.linga/tophat2/align_summary.txt
[2018-10-13 11:05:12] Run complete: 00:45:09 elapsed