[2018-10-13 17:01:24] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:01:24] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:01:24] Checking for Bowtie index files (genome)..
[2018-10-13 17:01:24] Checking for reference FASTA file
[2018-10-13 17:01:24] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:01:28] Reading known junctions from GTF file
[2018-10-13 17:01:32] Preparing reads
	 left reads: min. length=100, max. length=100, 439285 kept reads (373 discarded)
	right reads: min. length=100, max. length=100, 439029 kept reads (629 discarded)
[2018-10-13 17:01:50] Building transcriptome data files /scratch/8793382.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:02:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:10:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:10:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:11:25] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:11:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:12:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:12:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:12:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:12:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:12:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:13:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:13:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:14:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:14:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:14:24] Searching for junctions via segment mapping
[2018-10-13 17:17:16] Retrieving sequences for splices
[2018-10-13 17:19:15] Indexing splices
[2018-10-13 17:19:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:19:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:19:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:19:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:19:55] Joining segment hits
[2018-10-13 17:22:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:22:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:22:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:22:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:22:38] Joining segment hits
[2018-10-13 17:24:59] Reporting output tracks
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[2018-10-13 17:28:54] A summary of the alignment counts can be found in /scratch/8793382.1.linga/tophat2/align_summary.txt
[2018-10-13 17:28:54] Run complete: 00:27:29 elapsed