[2019-07-05 11:10:30] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:10:30] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:10:31] Checking for Bowtie index files (genome)..
[2019-07-05 11:10:31] Checking for reference FASTA file
[2019-07-05 11:10:31] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:10:34] Reading known junctions from GTF file
[2019-07-05 11:10:38] Preparing reads
	 left reads: min. length=150, max. length=150, 26148926 kept reads (2195 discarded)
	right reads: min. length=150, max. length=150, 26133008 kept reads (18113 discarded)
[2019-07-05 11:38:01] Building transcriptome data files /scratch/7534482.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:38:17] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:44:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:11:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:41:27] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:41:28] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:58:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:00:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:01:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:03:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:04:54] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:06:27] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:07:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:27:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:30:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:32:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:35:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:38:18] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:40:52] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:43:15] Searching for junctions via segment mapping
[2019-07-05 16:06:40] Retrieving sequences for splices
[2019-07-05 16:08:50] Indexing splices
[2019-07-05 16:10:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:11:58] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:13:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:14:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:16:03] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:17:20] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:18:29] Joining segment hits
[2019-07-05 16:24:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:26:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:28:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:31:12] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:33:25] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:35:27] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:37:21] Joining segment hits
[2019-07-05 16:44:39] Reporting output tracks
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[2019-07-05 18:31:12] A summary of the alignment counts can be found in /scratch/7534482.1.linga/tophat2/align_summary.txt
[2019-07-05 18:31:12] Run complete: 07:20:42 elapsed