[2018-10-13 06:37:41] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:37:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:37:41] Checking for Bowtie index files (genome)..
[2018-10-13 06:37:41] Checking for reference FASTA file
[2018-10-13 06:37:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:37:45] Reading known junctions from GTF file
[2018-10-13 06:37:49] Preparing reads
	 left reads: min. length=100, max. length=100, 1315788 kept reads (318 discarded)
	right reads: min. length=100, max. length=100, 1315360 kept reads (746 discarded)
[2018-10-13 06:38:43] Building transcriptome data files /scratch/8793060.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:39:03] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:47:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:50:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:54:02] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:54:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:54:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:55:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:55:25] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:55:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:55:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:56:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:56:58] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:57:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:57:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:57:59] Searching for junctions via segment mapping
[2018-10-13 07:09:26] Retrieving sequences for splices
[2018-10-13 07:11:37] Indexing splices
[2018-10-13 07:12:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:12:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:12:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:12:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:12:56] Joining segment hits
[2018-10-13 07:15:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:15:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:15:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:16:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:16:29] Joining segment hits
[2018-10-13 07:19:02] Reporting output tracks
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[2018-10-13 08:00:43] A summary of the alignment counts can be found in /scratch/8793060.1.linga/tophat2/align_summary.txt
[2018-10-13 08:00:43] Run complete: 01:23:02 elapsed