[2019-06-25 02:19:20] Beginning TopHat run (v2.1.1)
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[2019-06-25 02:19:20] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-25 02:19:20] Checking for Bowtie index files (genome)..
[2019-06-25 02:19:20] Checking for reference FASTA file
[2019-06-25 02:19:20] Generating SAM header for Bowtie2Index/genome
[2019-06-25 02:19:24] Reading known junctions from GTF file
[2019-06-25 02:19:28] Preparing reads
	 left reads: min. length=150, max. length=150, 69236229 kept reads (6124 discarded)
	right reads: min. length=150, max. length=150, 69225254 kept reads (17099 discarded)
[2019-06-25 03:46:51] Building transcriptome data files /scratch/7056837.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-25 03:47:13] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-25 03:54:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-25 04:47:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-25 05:43:26] Resuming TopHat pipeline with unmapped reads
[2019-06-25 05:43:27] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-25 07:48:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-25 08:05:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-25 08:23:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-25 08:41:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-25 08:59:21] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-25 09:12:05] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-25 09:17:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-25 11:13:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-25 11:33:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-25 11:53:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-25 12:12:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-25 12:31:50] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-25 12:46:57] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-25 12:55:45] Searching for junctions via segment mapping
[2019-06-26 00:09:48] Retrieving sequences for splices
[2019-06-26 00:12:42] Indexing splices
[2019-06-26 00:13:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-26 00:24:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-26 00:38:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-26 00:51:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-26 01:05:01] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-26 01:17:29] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-26 01:20:54] Joining segment hits
[2019-06-26 01:47:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-26 02:02:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-26 02:16:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-26 02:29:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-26 02:41:15] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-26 02:49:33] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-26 02:51:44] Joining segment hits
[2019-06-26 03:16:19] Reporting output tracks
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[2019-06-26 05:30:48] A summary of the alignment counts can be found in /scratch/7056837.1.linga/tophat2/align_summary.txt
[2019-06-26 05:30:48] Run complete: 1 days 03:11:27 elapsed