[2018-10-13 16:17:55] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:17:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:17:55] Checking for Bowtie index files (genome)..
[2018-10-13 16:17:55] Checking for reference FASTA file
[2018-10-13 16:17:55] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:18:01] Reading known junctions from GTF file
[2018-10-13 16:18:06] Preparing reads
	 left reads: min. length=100, max. length=100, 149238 kept reads (169 discarded)
	right reads: min. length=100, max. length=100, 149224 kept reads (183 discarded)
[2018-10-13 16:18:14] Building transcriptome data files /scratch/8793350.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:18:38] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:29:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:29:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:30:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:30:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:30:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:30:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:30:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:30:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:30:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:31:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:31:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:31:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:31:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:31:58] Searching for junctions via segment mapping
[2018-10-13 16:35:54] Retrieving sequences for splices
[2018-10-13 16:38:12] Indexing splices
[2018-10-13 16:38:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:38:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:38:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:38:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:38:55] Joining segment hits
[2018-10-13 16:42:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:42:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:42:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:42:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:42:26] Joining segment hits
[2018-10-13 16:45:09] Reporting output tracks
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[2018-10-13 16:49:03] A summary of the alignment counts can be found in /scratch/8793350.1.linga/tophat2/align_summary.txt
[2018-10-13 16:49:03] Run complete: 00:31:08 elapsed