[2019-06-26 14:21:28] Beginning TopHat run (v2.1.1)
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[2019-06-26 14:21:28] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 14:21:29] Checking for Bowtie index files (genome)..
[2019-06-26 14:21:29] Checking for reference FASTA file
[2019-06-26 14:21:29] Generating SAM header for Bowtie2Index/genome
[2019-06-26 14:21:33] Reading known junctions from GTF file
[2019-06-26 14:21:37] Preparing reads
	 left reads: min. length=35, max. length=76, 11143739 kept reads (251420 discarded)
	right reads: min. length=35, max. length=76, 11350854 kept reads (44305 discarded)
[2019-06-26 14:29:50] Building transcriptome data files /scratch/7076168.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 14:30:11] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 14:38:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 14:45:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 14:53:23] Resuming TopHat pipeline with unmapped reads
[2019-06-26 14:53:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 14:57:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 14:58:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 14:59:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 15:00:34] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 15:05:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 15:07:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 15:08:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 15:10:31] Searching for junctions via segment mapping
[2019-06-26 15:17:40] Retrieving sequences for splices
[2019-06-26 15:20:29] Indexing splices
[2019-06-26 15:20:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 15:21:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 15:21:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 15:22:03] Joining segment hits
[2019-06-26 15:25:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 15:26:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 15:26:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 15:27:33] Joining segment hits
[2019-06-26 15:31:30] Reporting output tracks
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[2019-06-26 17:14:50] A summary of the alignment counts can be found in /scratch/7076168.1.linga/tophat2/align_summary.txt
[2019-06-26 17:14:50] Run complete: 02:53:21 elapsed