[2018-10-13 00:00:00] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:00:00] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:00:00] Checking for Bowtie index files (genome)..
[2018-10-13 00:00:00] Checking for reference FASTA file
[2018-10-13 00:00:00] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:00:07] Reading known junctions from GTF file
[2018-10-13 00:00:13] Preparing reads
	 left reads: min. length=100, max. length=100, 397999 kept reads (269 discarded)
	right reads: min. length=100, max. length=100, 397655 kept reads (613 discarded)
[2018-10-13 00:00:37] Building transcriptome data files /scratch/8792852.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:01:02] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:10:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:11:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:11:41] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:11:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:12:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:12:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:12:53] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:13:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:13:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:13:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:14:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:14:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:14:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:14:57] Searching for junctions via segment mapping
[2018-10-13 00:18:48] Retrieving sequences for splices
[2018-10-13 00:23:17] Indexing splices
[2018-10-13 00:23:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:23:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:23:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:24:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:24:08] Joining segment hits
[2018-10-13 00:27:22] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:27:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:27:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:27:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:27:46] Joining segment hits
[2018-10-13 00:31:14] Reporting output tracks
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[2018-10-13 00:36:31] A summary of the alignment counts can be found in /scratch/8792852.1.linga/tophat2/align_summary.txt
[2018-10-13 00:36:32] Run complete: 00:36:31 elapsed