[2018-10-13 16:59:41] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:59:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:59:41] Checking for Bowtie index files (genome)..
[2018-10-13 16:59:41] Checking for reference FASTA file
[2018-10-13 16:59:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:59:45] Reading known junctions from GTF file
[2018-10-13 16:59:49] Preparing reads
	 left reads: min. length=100, max. length=100, 276575 kept reads (280 discarded)
	right reads: min. length=100, max. length=100, 276359 kept reads (496 discarded)
[2018-10-13 17:00:01] Building transcriptome data files /scratch/8793378.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:00:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:08:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:08:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:09:24] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:09:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:09:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:10:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:10:17] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:10:26] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:10:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:11:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:11:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:11:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:11:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:11:50] Searching for junctions via segment mapping
[2018-10-13 17:14:23] Retrieving sequences for splices
[2018-10-13 17:16:37] Indexing splices
[2018-10-13 17:16:56] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:17:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:17:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:17:08] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:17:12] Joining segment hits
[2018-10-13 17:19:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:19:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:19:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:19:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:19:47] Joining segment hits
[2018-10-13 17:22:07] Reporting output tracks
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[2018-10-13 17:25:14] A summary of the alignment counts can be found in /scratch/8793378.1.linga/tophat2/align_summary.txt
[2018-10-13 17:25:14] Run complete: 00:25:32 elapsed