[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 22:02:02] Reading known junctions from GTF file
[2018-10-12 22:02:07] Preparing reads
	 left reads: min. length=100, max. length=100, 519662 kept reads (396 discarded)
	right reads: min. length=100, max. length=100, 519304 kept reads (754 discarded)
[2018-10-12 22:02:30] Building transcriptome data files /scratch/8792779.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:02:51] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:11:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:12:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:13:34] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:13:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:14:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:14:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:14:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:14:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:15:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:15:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:16:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:16:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:16:37] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:16:49] Searching for junctions via segment mapping
[2018-10-12 22:19:50] Retrieving sequences for splices
[2018-10-12 22:22:05] Indexing splices
[2018-10-12 22:22:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:22:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:22:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:22:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:22:47] Joining segment hits
[2018-10-12 22:25:16] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:25:20] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:25:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:25:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:25:34] Joining segment hits
[2018-10-12 22:27:57] Reporting output tracks
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[2018-10-12 22:32:07] A summary of the alignment counts can be found in /scratch/8792779.1.linga/tophat2/align_summary.txt
[2018-10-12 22:32:07] Run complete: 00:30:09 elapsed