[2018-10-12 22:10:50] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:10:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:10:50] Checking for Bowtie index files (genome)..
[2018-10-12 22:10:50] Checking for reference FASTA file
[2018-10-12 22:10:50] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:10:54] Reading known junctions from GTF file
[2018-10-12 22:10:59] Preparing reads
	 left reads: min. length=100, max. length=100, 116695 kept reads (165 discarded)
	right reads: min. length=100, max. length=100, 116557 kept reads (303 discarded)
[2018-10-12 22:11:04] Building transcriptome data files /scratch/8792786.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:11:24] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:20:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:20:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:21:20] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:21:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:21:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:21:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:22:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:22:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:22:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:22:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:22:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:23:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:23:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:23:25] Searching for junctions via segment mapping
[2018-10-12 22:25:50] Retrieving sequences for splices
[2018-10-12 22:28:01] Indexing splices
[2018-10-12 22:28:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:28:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:28:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:28:33] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:28:37] Joining segment hits
[2018-10-12 22:31:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:31:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:31:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:31:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:31:18] Joining segment hits
[2018-10-12 22:33:38] Reporting output tracks
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[2018-10-12 22:36:12] A summary of the alignment counts can be found in /scratch/8792786.1.linga/tophat2/align_summary.txt
[2018-10-12 22:36:12] Run complete: 00:25:22 elapsed