[2018-10-13 05:43:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:43:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:43:31] Checking for Bowtie index files (genome)..
[2018-10-13 05:43:31] Checking for reference FASTA file
[2018-10-13 05:43:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:43:35] Reading known junctions from GTF file
[2018-10-13 05:43:40] Preparing reads
	 left reads: min. length=100, max. length=100, 1380635 kept reads (196 discarded)
	right reads: min. length=100, max. length=100, 1380184 kept reads (647 discarded)
[2018-10-13 05:44:46] Building transcriptome data files /scratch/8793031.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:45:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:53:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:55:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:57:59] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:57:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:58:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:59:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:59:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:59:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:00:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:00:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:01:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:01:34] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:01:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:02:05] Searching for junctions via segment mapping
[2018-10-13 06:11:12] Retrieving sequences for splices
[2018-10-13 06:13:21] Indexing splices
[2018-10-13 06:13:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:13:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:14:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:14:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:14:29] Joining segment hits
[2018-10-13 06:17:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:17:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:17:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:17:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:17:53] Joining segment hits
[2018-10-13 06:20:30] Reporting output tracks
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[2018-10-13 06:44:50] A summary of the alignment counts can be found in /scratch/8793031.1.linga/tophat2/align_summary.txt
[2018-10-13 06:44:50] Run complete: 01:01:19 elapsed