[2018-10-13 17:56:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:56:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:56:44] Checking for Bowtie index files (genome)..
[2018-10-13 17:56:44] Checking for reference FASTA file
[2018-10-13 17:56:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:56:49] Reading known junctions from GTF file
[2018-10-13 17:56:53] Preparing reads
	 left reads: min. length=100, max. length=100, 518279 kept reads (314 discarded)
	right reads: min. length=100, max. length=100, 517899 kept reads (694 discarded)
[2018-10-13 17:57:17] Building transcriptome data files /scratch/8793418.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:57:37] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:06:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:07:22] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:08:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:08:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:08:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:09:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:09:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:09:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:09:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:10:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:10:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:10:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:11:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:11:20] Searching for junctions via segment mapping
[2018-10-13 18:14:19] Retrieving sequences for splices
[2018-10-13 18:17:14] Indexing splices
[2018-10-13 18:17:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:17:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:17:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:17:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:17:52] Joining segment hits
[2018-10-13 18:20:56] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:21:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:21:06] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:21:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:21:15] Joining segment hits
[2018-10-13 18:23:45] Reporting output tracks
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[2018-10-13 18:27:48] A summary of the alignment counts can be found in /scratch/8793418.1.linga/tophat2/align_summary.txt
[2018-10-13 18:27:48] Run complete: 00:31:03 elapsed