[2018-10-12 21:08:46] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-12 21:08:46] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:08:46] Checking for Bowtie index files (genome)..
[2018-10-12 21:08:46] Checking for reference FASTA file
[2018-10-12 21:08:46] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:08:49] Reading known junctions from GTF file
[2018-10-12 21:08:52] Preparing reads
	 left reads: min. length=100, max. length=100, 169267 kept reads (88 discarded)
	right reads: min. length=100, max. length=100, 168803 kept reads (552 discarded)
[2018-10-12 21:08:57] Building transcriptome data files /scratch/8792745.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:09:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:16:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:16:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:16:47] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:16:47] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:17:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:17:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:17:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:17:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:17:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:17:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:17:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:17:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:17:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:17:53] Searching for junctions via segment mapping
[2018-10-12 21:19:03] Retrieving sequences for splices
[2018-10-12 21:20:08] Indexing splices
[2018-10-12 21:20:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:20:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:20:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:20:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:20:32] Joining segment hits
[2018-10-12 21:21:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:21:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:21:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:21:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:21:51] Joining segment hits
[2018-10-12 21:22:57] Reporting output tracks
-----------------------------------------------
[2018-10-12 21:24:18] A summary of the alignment counts can be found in /scratch/8792745.1.linga/tophat2/align_summary.txt
[2018-10-12 21:24:18] Run complete: 00:15:32 elapsed