[2018-10-13 16:37:04] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:37:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:37:04] Checking for Bowtie index files (genome)..
[2018-10-13 16:37:04] Checking for reference FASTA file
[2018-10-13 16:37:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:37:08] Reading known junctions from GTF file
[2018-10-13 16:37:12] Preparing reads
	 left reads: min. length=100, max. length=100, 266563 kept reads (167 discarded)
	right reads: min. length=100, max. length=100, 266390 kept reads (340 discarded)
[2018-10-13 16:37:25] Building transcriptome data files /scratch/8793365.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:37:45] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:46:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:46:40] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:47:06] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:47:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:47:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:47:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:47:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:47:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:48:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:48:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:48:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:48:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:49:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:49:10] Searching for junctions via segment mapping
[2018-10-13 16:51:50] Retrieving sequences for splices
[2018-10-13 16:53:52] Indexing splices
[2018-10-13 16:54:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:54:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:54:18] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:54:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:54:26] Joining segment hits
[2018-10-13 16:56:45] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:56:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:56:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:56:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:57:03] Joining segment hits
[2018-10-13 16:59:57] Reporting output tracks
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[2018-10-13 17:03:37] A summary of the alignment counts can be found in /scratch/8793365.1.linga/tophat2/align_summary.txt
[2018-10-13 17:03:37] Run complete: 00:26:33 elapsed