[2018-07-14 20:29:52] Beginning TopHat run (v2.1.1)
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[2018-07-14 20:29:52] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:29:53] Checking for Bowtie index files (genome)..
[2018-07-14 20:29:53] Checking for reference FASTA file
[2018-07-14 20:29:53] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:29:57] Reading known junctions from GTF file
[2018-07-14 20:30:01] Preparing reads
	 left reads: min. length=151, max. length=151, 18298009 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 18297654 kept reads (355 discarded)
[2018-07-14 20:49:02] Building transcriptome data files /scratch/6936772.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:49:22] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:57:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:14:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:31:56] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:31:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:03:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:13:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:24:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:34:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 22:43:02] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 22:47:30] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 22:51:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 23:27:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 23:37:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 23:48:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 23:58:55] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-15 00:08:58] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-15 00:16:36] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-15 00:21:01] Searching for junctions via segment mapping
[2018-07-15 07:19:42] Retrieving sequences for splices
[2018-07-15 07:21:56] Indexing splices
[2018-07-15 07:22:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 07:30:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 07:37:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 07:45:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 07:51:47] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 07:55:51] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 07:56:56] Joining segment hits
[2018-07-15 08:04:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 08:11:52] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 08:19:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 08:27:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 08:32:58] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 08:36:21] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 08:37:17] Joining segment hits
[2018-07-15 08:44:15] Reporting output tracks
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[2018-07-15 09:22:07] A summary of the alignment counts can be found in /scratch/6936772.1.linga/tophat2/align_summary.txt
[2018-07-15 09:22:07] Run complete: 12:52:14 elapsed