[2017-06-16 10:19:51] Beginning TopHat run (v2.1.1)
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[2017-06-16 10:19:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:19:52] Checking for Bowtie index files (genome)..
[2017-06-16 10:19:52] Checking for reference FASTA file
[2017-06-16 10:19:52] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:20:00] Reading known junctions from GTF file
[2017-06-16 10:20:05] Preparing reads
	 left reads: min. length=101, max. length=101, 17168634 kept reads (47 discarded)
	right reads: min. length=101, max. length=101, 17123480 kept reads (45201 discarded)
[2017-06-16 10:36:56] Building transcriptome data files /scratch/9351453.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 10:37:11] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 10:39:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:50:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 11:00:32] Resuming TopHat pipeline with unmapped reads
[2017-06-16 11:00:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:09:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:11:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:13:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:15:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:17:56] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:30:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:33:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:36:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:40:52] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:45:25] Searching for junctions via segment mapping
[2017-06-16 12:15:59] Retrieving sequences for splices
[2017-06-16 12:18:30] Indexing splices
[2017-06-16 12:19:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:20:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:22:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:23:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:25:11] Joining segment hits
[2017-06-16 12:29:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:30:52] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:32:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:34:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:36:10] Joining segment hits
[2017-06-16 12:40:35] Reporting output tracks
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[2017-06-16 13:04:46] A summary of the alignment counts can be found in /scratch/9351453.1.linga/tophat2/align_summary.txt
[2017-06-16 13:04:46] Run complete: 02:44:54 elapsed