[2019-09-04 11:19:45] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:19:45] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:19:45] Checking for Bowtie index files (genome)..
[2019-09-04 11:19:45] Checking for reference FASTA file
[2019-09-04 11:19:45] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:19:50] Reading known junctions from GTF file
[2019-09-04 11:19:53] Preparing reads
	 left reads: min. length=150, max. length=150, 30221098 kept reads (5 discarded)
	right reads: min. length=150, max. length=150, 30219942 kept reads (1161 discarded)
[2019-09-04 11:50:12] Building transcriptome data files /scratch/9142570.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:50:29] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:57:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:17:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 14:29:16] Resuming TopHat pipeline with unmapped reads
[2019-09-04 14:29:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 15:32:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 15:44:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:57:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 16:10:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 16:21:39] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 16:32:16] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 16:37:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 17:36:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 17:46:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 17:57:18] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 18:08:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 18:19:50] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 18:30:04] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 18:35:48] Searching for junctions via segment mapping
[2019-09-04 18:54:52] Retrieving sequences for splices
[2019-09-04 18:56:46] Indexing splices
[2019-09-04 18:57:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 19:01:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 19:04:10] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 19:07:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 19:11:13] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 19:14:15] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 19:16:00] Joining segment hits
[2019-09-04 19:25:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 19:28:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 19:30:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 19:32:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 19:36:42] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 19:39:31] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 19:41:59] Joining segment hits
[2019-09-04 19:52:39] Reporting output tracks
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[2019-09-04 20:42:17] A summary of the alignment counts can be found in /scratch/9142570.1.linga/tophat2/align_summary.txt
[2019-09-04 20:42:17] Run complete: 09:22:31 elapsed