[2018-10-12 21:01:55] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:01:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:01:55] Checking for Bowtie index files (genome)..
[2018-10-12 21:01:55] Checking for reference FASTA file
[2018-10-12 21:01:55] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:02:00] Reading known junctions from GTF file
[2018-10-12 21:02:04] Preparing reads
	 left reads: min. length=100, max. length=100, 182018 kept reads (50 discarded)
	right reads: min. length=100, max. length=100, 181935 kept reads (133 discarded)
[2018-10-12 21:02:15] Building transcriptome data files /scratch/8792739.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:02:36] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:11:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:12:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:12:22] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:12:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:12:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:12:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:13:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:13:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:13:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:13:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:13:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:13:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:14:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:14:14] Searching for junctions via segment mapping
[2018-10-12 21:16:45] Retrieving sequences for splices
[2018-10-12 21:19:08] Indexing splices
[2018-10-12 21:19:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:19:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:19:36] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:19:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:19:45] Joining segment hits
[2018-10-12 21:22:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:22:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:22:09] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:22:14] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:22:18] Joining segment hits
[2018-10-12 21:24:56] Reporting output tracks
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[2018-10-12 21:27:48] A summary of the alignment counts can be found in /scratch/8792739.1.linga/tophat2/align_summary.txt
[2018-10-12 21:27:48] Run complete: 00:25:53 elapsed