[2018-10-12 22:21:28] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:21:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:21:28] Checking for Bowtie index files (genome)..
[2018-10-12 22:21:28] Checking for reference FASTA file
[2018-10-12 22:21:28] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:21:33] Reading known junctions from GTF file
[2018-10-12 22:21:38] Preparing reads
	 left reads: min. length=100, max. length=100, 267520 kept reads (260 discarded)
	right reads: min. length=100, max. length=100, 267266 kept reads (514 discarded)
[2018-10-12 22:21:50] Building transcriptome data files /scratch/8792791.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:22:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:30:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:31:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:31:51] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:31:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:32:34] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:32:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:32:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:33:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:33:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:34:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:34:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:34:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:34:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:34:45] Searching for junctions via segment mapping
[2018-10-12 22:37:20] Retrieving sequences for splices
[2018-10-12 22:39:36] Indexing splices
[2018-10-12 22:40:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:40:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:40:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:40:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:40:16] Joining segment hits
[2018-10-12 22:42:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:42:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:42:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:42:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:42:57] Joining segment hits
[2018-10-12 22:45:19] Reporting output tracks
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[2018-10-12 22:48:32] A summary of the alignment counts can be found in /scratch/8792791.1.linga/tophat2/align_summary.txt
[2018-10-12 22:48:32] Run complete: 00:27:04 elapsed