[2017-06-16 10:20:27] Beginning TopHat run (v2.1.1)
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[2017-06-16 10:20:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:20:27] Checking for Bowtie index files (genome)..
[2017-06-16 10:20:27] Checking for reference FASTA file
[2017-06-16 10:20:27] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:20:32] Reading known junctions from GTF file
[2017-06-16 10:20:34] Preparing reads
	 left reads: min. length=101, max. length=101, 63218600 kept reads (313738 discarded)
	right reads: min. length=101, max. length=101, 63417839 kept reads (114499 discarded)
[2017-06-16 11:36:47] Building transcriptome data files /scratch/9351451.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 11:37:05] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 11:39:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 12:24:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 13:04:30] Resuming TopHat pipeline with unmapped reads
[2017-06-16 13:04:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 13:36:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 13:43:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 13:50:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 13:57:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 14:05:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 14:37:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 14:44:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 14:53:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 15:05:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 15:15:59] Searching for junctions via segment mapping
[2017-06-16 17:43:42] Retrieving sequences for splices
[2017-06-16 17:46:04] Indexing splices
[2017-06-16 17:47:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 17:58:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 18:09:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 18:20:02] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 18:30:27] Joining segment hits
[2017-06-16 18:37:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 18:48:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 18:59:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 19:09:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 19:20:23] Joining segment hits
[2017-06-16 19:27:43] Reporting output tracks
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[2017-06-16 20:42:30] A summary of the alignment counts can be found in /scratch/9351451.1.linga/tophat2/align_summary.txt
[2017-06-16 20:42:30] Run complete: 10:22:02 elapsed