[2017-06-16 10:20:08] Beginning TopHat run (v2.1.1)
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[2017-06-16 10:20:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:20:08] Checking for Bowtie index files (genome)..
[2017-06-16 10:20:08] Checking for reference FASTA file
[2017-06-16 10:20:08] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:20:14] Reading known junctions from GTF file
[2017-06-16 10:20:16] Preparing reads
	 left reads: min. length=101, max. length=101, 17627982 kept reads (43 discarded)
	right reads: min. length=101, max. length=101, 17583101 kept reads (44924 discarded)
[2017-06-16 10:36:48] Building transcriptome data files /scratch/9351459.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 10:37:03] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 10:38:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:50:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 11:01:33] Resuming TopHat pipeline with unmapped reads
[2017-06-16 11:01:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:11:52] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:13:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:15:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:17:52] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:20:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:33:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:36:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:39:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:42:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:46:43] Searching for junctions via segment mapping
[2017-06-16 12:16:59] Retrieving sequences for splices
[2017-06-16 12:19:19] Indexing splices
[2017-06-16 12:20:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:21:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:23:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:24:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:26:17] Joining segment hits
[2017-06-16 12:30:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:32:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:34:10] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:35:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:37:54] Joining segment hits
[2017-06-16 12:42:16] Reporting output tracks
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[2017-06-16 13:06:17] A summary of the alignment counts can be found in /scratch/9351459.1.linga/tophat2/align_summary.txt
[2017-06-16 13:06:17] Run complete: 02:46:08 elapsed