[2017-06-16 10:19:49] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2017-06-16 10:19:49] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:19:49] Checking for Bowtie index files (genome)..
[2017-06-16 10:19:49] Checking for reference FASTA file
[2017-06-16 10:19:49] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:19:53] Reading known junctions from GTF file
[2017-06-16 10:19:56] Preparing reads
	 left reads: min. length=101, max. length=101, 16152240 kept reads (41 discarded)
	right reads: min. length=101, max. length=101, 16106035 kept reads (46246 discarded)
[2017-06-16 10:33:38] Building transcriptome data files /scratch/9351454.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 10:33:54] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 10:35:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:44:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:54:30] Resuming TopHat pipeline with unmapped reads
[2017-06-16 10:54:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:06:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:09:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:11:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:13:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:17:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:31:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:34:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:38:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:47:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:52:23] Searching for junctions via segment mapping
[2017-06-16 12:18:18] Retrieving sequences for splices
[2017-06-16 12:20:44] Indexing splices
[2017-06-16 12:21:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:22:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:24:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:25:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:27:03] Joining segment hits
[2017-06-16 12:30:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:32:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:34:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:36:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:37:42] Joining segment hits
[2017-06-16 12:42:08] Reporting output tracks
-----------------------------------------------
[2017-06-16 13:01:40] A summary of the alignment counts can be found in /scratch/9351454.1.linga/tophat2/align_summary.txt
[2017-06-16 13:01:40] Run complete: 02:41:51 elapsed