[2018-10-13 14:08:02] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 14:08:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:08:02] Checking for Bowtie index files (genome)..
[2018-10-13 14:08:02] Checking for reference FASTA file
[2018-10-13 14:08:02] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:08:06] Reading known junctions from GTF file
[2018-10-13 14:08:11] Preparing reads
	 left reads: min. length=100, max. length=100, 1017511 kept reads (79 discarded)
	right reads: min. length=100, max. length=100, 1017327 kept reads (263 discarded)
[2018-10-13 14:09:01] Building transcriptome data files /scratch/8793281.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:09:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:17:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:18:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:19:37] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:19:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:20:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:20:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:20:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:20:56] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:21:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:21:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:22:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:22:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:22:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:22:52] Searching for junctions via segment mapping
[2018-10-13 14:26:45] Retrieving sequences for splices
[2018-10-13 14:28:49] Indexing splices
[2018-10-13 14:29:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:29:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:29:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:29:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:29:34] Joining segment hits
[2018-10-13 14:31:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:31:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:32:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:32:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:32:17] Joining segment hits
[2018-10-13 14:34:46] Reporting output tracks
-----------------------------------------------
[2018-10-13 14:42:24] A summary of the alignment counts can be found in /scratch/8793281.1.linga/tophat2/align_summary.txt
[2018-10-13 14:42:24] Run complete: 00:34:22 elapsed