[2017-06-14 21:34:35] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:35] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:35] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:35] Checking for reference FASTA file
[2017-06-14 21:34:35] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:40] Reading known junctions from GTF file
[2017-06-14 21:34:43] Preparing reads
	 left reads: min. length=101, max. length=101, 21483486 kept reads (5272 discarded)
	right reads: min. length=101, max. length=101, 21469999 kept reads (18759 discarded)
[2017-06-14 21:58:33] Building transcriptome data files /scratch/9328368.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:58:50] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 22:01:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:15:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:29:58] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:29:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:43:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:46:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:49:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:52:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:56:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 23:11:41] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 23:14:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 23:17:46] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 23:21:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:25:15] Searching for junctions via segment mapping
[2017-06-15 00:19:33] Retrieving sequences for splices
[2017-06-15 00:21:57] Indexing splices
[2017-06-15 00:22:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-15 00:25:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-15 00:28:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-15 00:31:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-15 00:34:36] Joining segment hits
[2017-06-15 00:39:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-15 00:42:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-15 00:45:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-15 00:48:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-15 00:51:19] Joining segment hits
[2017-06-15 00:56:13] Reporting output tracks
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[2017-06-15 01:25:56] A summary of the alignment counts can be found in /scratch/9328368.1.linga/tophat2/align_summary.txt
[2017-06-15 01:25:56] Run complete: 03:51:20 elapsed