[2018-10-13 03:10:01] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:10:01] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:10:01] Checking for Bowtie index files (genome)..
[2018-10-13 03:10:01] Checking for reference FASTA file
[2018-10-13 03:10:01] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:10:05] Reading known junctions from GTF file
[2018-10-13 03:10:10] Preparing reads
	 left reads: min. length=100, max. length=100, 325067 kept reads (139 discarded)
	right reads: min. length=100, max. length=100, 324884 kept reads (322 discarded)
[2018-10-13 03:10:25] Building transcriptome data files /scratch/8792944.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:10:45] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:19:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:19:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:20:08] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:20:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:20:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:20:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:21:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:21:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:21:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:21:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:22:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:22:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:22:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:22:39] Searching for junctions via segment mapping
[2018-10-13 03:25:29] Retrieving sequences for splices
[2018-10-13 03:27:38] Indexing splices
[2018-10-13 03:27:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:28:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:28:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:28:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:28:17] Joining segment hits
[2018-10-13 03:30:45] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:30:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:30:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:30:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:31:03] Joining segment hits
[2018-10-13 03:33:29] Reporting output tracks
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[2018-10-13 03:37:33] A summary of the alignment counts can be found in /scratch/8792944.1.linga/tophat2/align_summary.txt
[2018-10-13 03:37:33] Run complete: 00:27:31 elapsed