[2019-06-26 09:48:52] Beginning TopHat run (v2.1.1)
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[2019-06-26 09:48:52] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 09:48:53] Checking for Bowtie index files (genome)..
[2019-06-26 09:48:53] Checking for reference FASTA file
[2019-06-26 09:48:53] Generating SAM header for Bowtie2Index/genome
[2019-06-26 09:48:55] Reading known junctions from GTF file
[2019-06-26 09:48:59] Preparing reads
	 left reads: min. length=51, max. length=51, 17461089 kept reads (39634 discarded)
	right reads: min. length=51, max. length=51, 17490637 kept reads (10086 discarded)
[2019-06-26 09:58:00] Building transcriptome data files /scratch/7076160.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 09:58:17] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 10:05:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 10:15:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 10:26:36] Resuming TopHat pipeline with unmapped reads
[2019-06-26 10:26:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 10:32:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 10:33:39] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 10:34:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 10:39:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 10:39:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 10:40:49] Searching for junctions via segment mapping
[2019-06-26 10:45:34] Retrieving sequences for splices
[2019-06-26 10:47:51] Indexing splices
[2019-06-26 10:48:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 10:48:15] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 10:48:22] Joining segment hits
[2019-06-26 10:51:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 10:51:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 10:51:29] Joining segment hits
[2019-06-26 10:54:15] Reporting output tracks
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[2019-06-26 15:07:15] A summary of the alignment counts can be found in /scratch/7076160.1.linga/tophat2/align_summary.txt
[2019-06-26 15:07:15] Run complete: 05:18:23 elapsed