[2018-10-13 09:11:35] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:11:35] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:11:35] Checking for Bowtie index files (genome)..
[2018-10-13 09:11:35] Checking for reference FASTA file
[2018-10-13 09:11:35] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:11:40] Reading known junctions from GTF file
[2018-10-13 09:11:44] Preparing reads
	 left reads: min. length=100, max. length=100, 1131519 kept reads (68 discarded)
	right reads: min. length=100, max. length=100, 1131097 kept reads (490 discarded)
[2018-10-13 09:12:29] Building transcriptome data files /scratch/8793139.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:12:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:21:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:21:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:22:48] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:22:48] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:23:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:23:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:23:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:23:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:24:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:24:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:24:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:24:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:25:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:25:19] Searching for junctions via segment mapping
[2018-10-13 09:29:09] Retrieving sequences for splices
[2018-10-13 09:31:08] Indexing splices
[2018-10-13 09:31:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:31:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:31:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:31:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:31:54] Joining segment hits
[2018-10-13 09:34:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:34:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:34:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:34:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:34:42] Joining segment hits
[2018-10-13 09:37:20] Reporting output tracks
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[2018-10-13 09:47:28] A summary of the alignment counts can be found in /scratch/8793139.1.linga/tophat2/align_summary.txt
[2018-10-13 09:47:28] Run complete: 00:35:53 elapsed