[2018-07-14 20:21:15] Beginning TopHat run (v2.1.1)
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[2018-07-14 20:21:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-07-14 20:21:15] Checking for Bowtie index files (genome)..
[2018-07-14 20:21:15] Checking for reference FASTA file
[2018-07-14 20:21:15] Generating SAM header for Bowtie2Index/genome
[2018-07-14 20:21:19] Reading known junctions from GTF file
[2018-07-14 20:21:23] Preparing reads
	 left reads: min. length=151, max. length=151, 20703604 kept reads (0 discarded)
	right reads: min. length=151, max. length=151, 20703231 kept reads (373 discarded)
[2018-07-14 20:44:43] Building transcriptome data files /scratch/6936766.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-07-14 20:45:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-07-14 20:53:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:15:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-07-14 21:37:58] Resuming TopHat pipeline with unmapped reads
[2018-07-14 21:37:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 22:12:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-14 22:25:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-14 22:39:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-14 22:54:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-14 23:05:40] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-14 23:12:00] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-14 23:16:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-07-14 23:56:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2018-07-15 00:10:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2018-07-15 00:24:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2018-07-15 00:40:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2018-07-15 00:56:08] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2018-07-15 01:07:32] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2018-07-15 01:14:11] Searching for junctions via segment mapping
[2018-07-15 13:29:29] Retrieving sequences for splices
[2018-07-15 13:31:23] Indexing splices
[2018-07-15 13:32:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 13:44:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 13:57:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 14:09:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 14:20:29] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 14:27:06] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 14:28:28] Joining segment hits
[2018-07-15 14:37:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2018-07-15 14:50:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2018-07-15 15:04:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2018-07-15 15:17:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2018-07-15 15:28:25] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2018-07-15 15:35:28] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2018-07-15 15:37:10] Joining segment hits
[2018-07-15 15:46:38] Reporting output tracks
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[2018-07-15 17:13:22] A summary of the alignment counts can be found in /scratch/6936766.1.linga/tophat2/align_summary.txt
[2018-07-15 17:13:22] Run complete: 20:52:07 elapsed