[2018-10-13 00:01:36] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 00:01:36] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:01:36] Checking for Bowtie index files (genome)..
[2018-10-13 00:01:36] Checking for reference FASTA file
[2018-10-13 00:01:36] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:01:41] Reading known junctions from GTF file
[2018-10-13 00:01:45] Preparing reads
	 left reads: min. length=100, max. length=100, 234233 kept reads (199 discarded)
	right reads: min. length=100, max. length=100, 233981 kept reads (451 discarded)
[2018-10-13 00:01:56] Building transcriptome data files /scratch/8792853.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:02:15] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:10:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:10:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:11:28] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:11:28] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:12:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:12:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:12:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:12:30] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:12:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:13:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:13:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:13:35] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:13:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:13:55] Searching for junctions via segment mapping
[2018-10-13 00:16:25] Retrieving sequences for splices
[2018-10-13 00:18:32] Indexing splices
[2018-10-13 00:18:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:18:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:19:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:19:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:19:09] Joining segment hits
[2018-10-13 00:21:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:21:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:21:33] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:21:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:21:41] Joining segment hits
[2018-10-13 00:23:56] Reporting output tracks
-----------------------------------------------
[2018-10-13 00:26:58] A summary of the alignment counts can be found in /scratch/8792853.1.linga/tophat2/align_summary.txt
[2018-10-13 00:26:58] Run complete: 00:25:22 elapsed