[2018-10-13 14:30:48] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:30:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:30:48] Checking for Bowtie index files (genome)..
[2018-10-13 14:30:48] Checking for reference FASTA file
[2018-10-13 14:30:48] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:30:52] Reading known junctions from GTF file
[2018-10-13 14:30:57] Preparing reads
	 left reads: min. length=100, max. length=100, 406430 kept reads (43 discarded)
	right reads: min. length=100, max. length=100, 406249 kept reads (224 discarded)
[2018-10-13 14:31:14] Building transcriptome data files /scratch/8793293.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:31:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:39:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:40:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:40:38] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:40:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:40:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:41:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:41:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:41:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:41:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:41:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:41:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:42:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:42:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:42:25] Searching for junctions via segment mapping
[2018-10-13 14:45:17] Retrieving sequences for splices
[2018-10-13 14:47:26] Indexing splices
[2018-10-13 14:47:46] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:47:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:47:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:48:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:48:04] Joining segment hits
[2018-10-13 14:50:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:50:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:50:33] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:50:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:50:42] Joining segment hits
[2018-10-13 14:52:55] Reporting output tracks
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[2018-10-13 14:56:25] A summary of the alignment counts can be found in /scratch/8793293.1.linga/tophat2/align_summary.txt
[2018-10-13 14:56:25] Run complete: 00:25:36 elapsed