[2017-06-14 21:34:22] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:22] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:23] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:23] Checking for reference FASTA file
[2017-06-14 21:34:23] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:27] Reading known junctions from GTF file
[2017-06-14 21:34:30] Preparing reads
	 left reads: min. length=101, max. length=101, 16088776 kept reads (5836 discarded)
	right reads: min. length=101, max. length=101, 16081103 kept reads (13509 discarded)
[2017-06-14 21:51:29] Building transcriptome data files /scratch/9328371.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:51:45] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:53:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:03:51] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:14:06] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:14:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:22:35] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:24:14] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:25:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:27:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:30:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:42:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:43:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:46:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:48:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:51:01] Searching for junctions via segment mapping
[2017-06-14 23:17:55] Retrieving sequences for splices
[2017-06-14 23:20:28] Indexing splices
[2017-06-14 23:21:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:22:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:24:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:25:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:26:47] Joining segment hits
[2017-06-14 23:31:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:32:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:33:46] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:35:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:36:32] Joining segment hits
[2017-06-14 23:40:40] Reporting output tracks
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[2017-06-15 00:08:13] A summary of the alignment counts can be found in /scratch/9328371.1.linga/tophat2/align_summary.txt
[2017-06-15 00:08:13] Run complete: 02:33:50 elapsed