[2019-06-28 13:24:58] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:24:58] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:24:59] Checking for Bowtie index files (genome)..
[2019-06-28 13:24:59] Checking for reference FASTA file
[2019-06-28 13:24:59] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:25:05] Reading known junctions from GTF file
[2019-06-28 13:25:09] Preparing reads
	 left reads: min. length=150, max. length=150, 27561186 kept reads (528 discarded)
	right reads: min. length=150, max. length=150, 27561589 kept reads (125 discarded)
[2019-06-28 13:55:50] Building transcriptome data files /scratch/7287271.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:56:09] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:03:13] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:28:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:53:29] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:53:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:36:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:43:20] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:50:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:57:35] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:04:24] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:09:47] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:12:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 17:01:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 17:09:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 17:17:18] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 17:24:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 17:32:38] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:39:04] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:42:16] Searching for junctions via segment mapping
[2019-06-29 02:26:11] Retrieving sequences for splices
[2019-06-29 02:29:44] Indexing splices
[2019-06-29 02:32:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 02:39:53] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 02:48:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 02:56:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 03:08:21] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 03:15:30] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 03:17:25] Joining segment hits
[2019-06-29 03:36:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 03:45:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 03:53:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 04:03:12] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 04:10:59] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 04:17:45] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 04:19:39] Joining segment hits
[2019-06-29 04:36:33] Reporting output tracks
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[2019-06-29 06:24:10] A summary of the alignment counts can be found in /scratch/7287271.1.linga/tophat2/align_summary.txt
[2019-06-29 06:24:10] Run complete: 16:59:11 elapsed