[2018-10-12 22:29:53] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:29:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:29:53] Checking for Bowtie index files (genome)..
[2018-10-12 22:29:53] Checking for reference FASTA file
[2018-10-12 22:29:53] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:29:57] Reading known junctions from GTF file
[2018-10-12 22:30:05] Preparing reads
	 left reads: min. length=100, max. length=100, 404641 kept reads (236 discarded)
	right reads: min. length=100, max. length=100, 404288 kept reads (589 discarded)
[2018-10-12 22:30:38] Building transcriptome data files /scratch/8792793.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:30:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:41:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:41:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:42:47] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:42:47] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:43:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:43:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:44:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:44:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:44:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:45:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:45:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:45:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:46:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:46:11] Searching for junctions via segment mapping
[2018-10-12 22:49:12] Retrieving sequences for splices
[2018-10-12 22:52:52] Indexing splices
[2018-10-12 22:53:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:53:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:53:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:53:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:53:42] Joining segment hits
[2018-10-12 22:56:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:56:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:56:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:56:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:56:43] Joining segment hits
[2018-10-12 23:00:07] Reporting output tracks
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[2018-10-12 23:05:17] A summary of the alignment counts can be found in /scratch/8792793.1.linga/tophat2/align_summary.txt
[2018-10-12 23:05:17] Run complete: 00:35:24 elapsed