[2019-07-17 22:24:24] Beginning TopHat run (v2.1.1)
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[2019-07-17 22:24:24] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 22:24:25] Checking for Bowtie index files (genome)..
[2019-07-17 22:24:25] Checking for reference FASTA file
[2019-07-17 22:24:25] Generating SAM header for Bowtie2Index/genome
[2019-07-17 22:24:29] Reading known junctions from GTF file
[2019-07-17 22:24:33] Preparing reads
	 left reads: min. length=150, max. length=150, 29217798 kept reads (467 discarded)
	right reads: min. length=150, max. length=150, 29218124 kept reads (141 discarded)
[2019-07-17 22:54:04] Building transcriptome data files /scratch/7776704.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 22:54:21] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 23:00:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 23:25:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 23:52:25] Resuming TopHat pipeline with unmapped reads
[2019-07-17 23:52:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 00:28:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 00:35:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 00:43:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 00:51:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 00:59:29] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 01:05:46] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 01:08:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 01:51:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 01:59:50] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 02:08:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 02:16:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 02:25:30] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 02:32:22] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 02:35:32] Searching for junctions via segment mapping
[2019-07-18 11:57:15] Retrieving sequences for splices
[2019-07-18 11:59:28] Indexing splices
[2019-07-18 12:01:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 12:10:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 12:19:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 12:28:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 12:38:11] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 12:45:17] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 12:47:16] Joining segment hits
[2019-07-18 13:02:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 13:12:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 13:22:21] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 13:32:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 13:41:49] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 13:48:58] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 13:50:58] Joining segment hits
[2019-07-18 14:08:33] Reporting output tracks
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[2019-07-18 15:56:04] A summary of the alignment counts can be found in /scratch/7776704.1.linga/tophat2/align_summary.txt
[2019-07-18 15:56:04] Run complete: 17:31:40 elapsed