[2018-10-13 15:56:46] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:56:46] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:56:46] Checking for Bowtie index files (genome)..
[2018-10-13 15:56:46] Checking for reference FASTA file
[2018-10-13 15:56:46] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:56:50] Reading known junctions from GTF file
[2018-10-13 15:56:55] Preparing reads
	 left reads: min. length=100, max. length=100, 187051 kept reads (206 discarded)
	right reads: min. length=100, max. length=100, 187038 kept reads (219 discarded)
[2018-10-13 15:57:03] Building transcriptome data files /scratch/8793339.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:57:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:05:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:06:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:06:41] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:06:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:07:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:07:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:07:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:07:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:07:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:08:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:08:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:08:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:08:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:08:58] Searching for junctions via segment mapping
[2018-10-13 16:11:28] Retrieving sequences for splices
[2018-10-13 16:13:42] Indexing splices
[2018-10-13 16:14:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:14:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:14:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:14:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:14:20] Joining segment hits
[2018-10-13 16:16:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:16:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:16:46] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:16:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:16:54] Joining segment hits
[2018-10-13 16:19:19] Reporting output tracks
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[2018-10-13 16:22:18] A summary of the alignment counts can be found in /scratch/8793339.1.linga/tophat2/align_summary.txt
[2018-10-13 16:22:18] Run complete: 00:25:32 elapsed