[2018-10-12 22:01:58] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:01:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:01:58] Checking for Bowtie index files (genome)..
[2018-10-12 22:01:58] Checking for reference FASTA file
[2018-10-12 22:01:58] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:02:03] Reading known junctions from GTF file
[2018-10-12 22:02:08] Preparing reads
	 left reads: min. length=100, max. length=100, 431979 kept reads (203 discarded)
	right reads: min. length=100, max. length=100, 431682 kept reads (500 discarded)
[2018-10-12 22:02:27] Building transcriptome data files /scratch/8792776.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:02:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:11:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:12:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:12:53] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:12:53] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:13:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:13:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:14:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:14:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:14:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:15:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:15:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:15:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:15:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:16:04] Searching for junctions via segment mapping
[2018-10-12 22:18:59] Retrieving sequences for splices
[2018-10-12 22:21:16] Indexing splices
[2018-10-12 22:21:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:21:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:21:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:21:52] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:21:56] Joining segment hits
[2018-10-12 22:24:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:24:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:24:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:24:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:24:49] Joining segment hits
[2018-10-12 22:27:29] Reporting output tracks
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[2018-10-12 22:31:19] A summary of the alignment counts can be found in /scratch/8792776.1.linga/tophat2/align_summary.txt
[2018-10-12 22:31:19] Run complete: 00:29:21 elapsed