[2019-07-10 19:23:19] Beginning TopHat run (v2.1.1)
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[2019-07-10 19:23:19] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-10 19:23:20] Checking for Bowtie index files (genome)..
[2019-07-10 19:23:20] Checking for reference FASTA file
[2019-07-10 19:23:20] Generating SAM header for Bowtie2Index/genome
[2019-07-10 19:23:22] Reading known junctions from GTF file
[2019-07-10 19:23:25] Preparing reads
	 left reads: min. length=150, max. length=150, 21739240 kept reads (1707 discarded)
	right reads: min. length=150, max. length=150, 21726171 kept reads (14776 discarded)
[2019-07-10 19:43:19] Building transcriptome data files /scratch/7651019.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-10 19:43:29] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-10 19:47:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-10 20:00:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-10 20:14:15] Resuming TopHat pipeline with unmapped reads
[2019-07-10 20:14:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-10 20:22:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-10 20:22:45] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-10 20:23:34] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-10 20:24:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-10 20:25:15] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-10 20:26:04] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-10 20:26:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-10 20:36:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-10 20:37:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-10 20:38:46] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-10 20:40:04] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-10 20:41:15] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-10 20:42:25] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-10 20:43:36] Searching for junctions via segment mapping
[2019-07-10 21:50:05] Retrieving sequences for splices
[2019-07-10 21:51:11] Indexing splices
[2019-07-10 21:52:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-10 21:52:52] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-10 21:53:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-10 21:54:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-10 21:54:56] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-10 21:55:36] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-10 21:56:13] Joining segment hits
[2019-07-10 21:58:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-10 21:59:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-10 22:00:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-10 22:02:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-10 22:03:11] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-10 22:04:10] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-10 22:05:03] Joining segment hits
[2019-07-10 22:08:07] Reporting output tracks
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[2019-07-10 22:53:07] A summary of the alignment counts can be found in /scratch/7651019.1.linga/tophat2/align_summary.txt
[2019-07-10 22:53:07] Run complete: 03:29:47 elapsed