[2018-10-13 06:06:46] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:06:46] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:06:46] Checking for Bowtie index files (genome)..
[2018-10-13 06:06:46] Checking for reference FASTA file
[2018-10-13 06:06:46] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:06:50] Reading known junctions from GTF file
[2018-10-13 06:06:55] Preparing reads
	 left reads: min. length=100, max. length=100, 306833 kept reads (227 discarded)
	right reads: min. length=100, max. length=100, 306441 kept reads (619 discarded)
[2018-10-13 06:07:09] Building transcriptome data files /scratch/8793045.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:07:28] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:16:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:16:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:17:02] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:17:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:17:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:17:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:17:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:17:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:17:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:18:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:18:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:18:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:18:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:18:58] Searching for junctions via segment mapping
[2018-10-13 06:21:49] Retrieving sequences for splices
[2018-10-13 06:23:59] Indexing splices
[2018-10-13 06:24:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:24:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:24:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:24:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:24:35] Joining segment hits
[2018-10-13 06:27:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:27:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:27:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:27:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:27:22] Joining segment hits
[2018-10-13 06:29:45] Reporting output tracks
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[2018-10-13 06:33:46] A summary of the alignment counts can be found in /scratch/8793045.1.linga/tophat2/align_summary.txt
[2018-10-13 06:33:46] Run complete: 00:26:59 elapsed