[2018-10-13 00:06:42] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:06:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:06:42] Checking for Bowtie index files (genome)..
[2018-10-13 00:06:42] Checking for reference FASTA file
[2018-10-13 00:06:42] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:06:46] Reading known junctions from GTF file
[2018-10-13 00:06:50] Preparing reads
	 left reads: min. length=100, max. length=100, 2499130 kept reads (839 discarded)
	right reads: min. length=100, max. length=100, 2498385 kept reads (1584 discarded)
[2018-10-13 00:08:34] Building transcriptome data files /scratch/8792855.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:08:54] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:17:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:19:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:22:26] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:22:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:24:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:25:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:26:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:26:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:27:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:29:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:30:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:31:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:31:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:32:30] Searching for junctions via segment mapping
[2018-10-13 00:42:01] Retrieving sequences for splices
[2018-10-13 00:44:27] Indexing splices
[2018-10-13 00:44:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:45:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:45:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:45:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:45:55] Joining segment hits
[2018-10-13 00:48:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:48:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:49:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:49:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:49:48] Joining segment hits
[2018-10-13 00:52:44] Reporting output tracks
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[2018-10-13 01:16:50] A summary of the alignment counts can be found in /scratch/8792855.1.linga/tophat2/align_summary.txt
[2018-10-13 01:16:50] Run complete: 01:10:08 elapsed