[2018-10-13 18:03:23] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:03:23] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:03:23] Checking for Bowtie index files (genome)..
[2018-10-13 18:03:23] Checking for reference FASTA file
[2018-10-13 18:03:23] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:03:27] Reading known junctions from GTF file
[2018-10-13 18:03:32] Preparing reads
	 left reads: min. length=100, max. length=100, 463266 kept reads (188 discarded)
	right reads: min. length=100, max. length=100, 462999 kept reads (455 discarded)
[2018-10-13 18:03:53] Building transcriptome data files /scratch/8793425.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:04:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:12:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:13:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:13:41] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:13:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:14:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:14:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:14:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:14:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:14:56] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:15:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:15:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:15:54] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:16:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:16:15] Searching for junctions via segment mapping
[2018-10-13 18:19:12] Retrieving sequences for splices
[2018-10-13 18:21:24] Indexing splices
[2018-10-13 18:21:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:21:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:21:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:22:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:22:04] Joining segment hits
[2018-10-13 18:24:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:24:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:24:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:24:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:24:47] Joining segment hits
[2018-10-13 18:27:10] Reporting output tracks
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[2018-10-13 18:31:00] A summary of the alignment counts can be found in /scratch/8793425.1.linga/tophat2/align_summary.txt
[2018-10-13 18:31:00] Run complete: 00:27:37 elapsed