[2018-10-13 03:13:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:13:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:13:10] Checking for Bowtie index files (genome)..
[2018-10-13 03:13:10] Checking for reference FASTA file
[2018-10-13 03:13:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:13:14] Reading known junctions from GTF file
[2018-10-13 03:13:19] Preparing reads
	 left reads: min. length=100, max. length=100, 370178 kept reads (233 discarded)
	right reads: min. length=100, max. length=100, 369859 kept reads (552 discarded)
[2018-10-13 03:13:35] Building transcriptome data files /scratch/8792946.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:13:55] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:21:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:22:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:23:13] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:23:13] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:23:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:24:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:24:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:24:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:24:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:25:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:25:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:25:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:25:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:26:10] Searching for junctions via segment mapping
[2018-10-13 03:28:49] Retrieving sequences for splices
[2018-10-13 03:30:58] Indexing splices
[2018-10-13 03:31:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:31:20] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:31:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:31:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:31:33] Joining segment hits
[2018-10-13 03:33:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:33:55] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:34:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:34:04] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:34:09] Joining segment hits
[2018-10-13 03:36:27] Reporting output tracks
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[2018-10-13 03:39:40] A summary of the alignment counts can be found in /scratch/8792946.1.linga/tophat2/align_summary.txt
[2018-10-13 03:39:40] Run complete: 00:26:30 elapsed