[2019-06-26 12:52:26] Beginning TopHat run (v2.1.1)
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[2019-06-26 12:52:26] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 12:52:26] Checking for Bowtie index files (genome)..
[2019-06-26 12:52:26] Checking for reference FASTA file
[2019-06-26 12:52:26] Generating SAM header for Bowtie2Index/genome
[2019-06-26 12:52:31] Reading known junctions from GTF file
[2019-06-26 12:52:36] Preparing reads
	 left reads: min. length=51, max. length=51, 24194001 kept reads (44538 discarded)
	right reads: min. length=51, max. length=51, 24226468 kept reads (12071 discarded)
[2019-06-26 13:08:27] Building transcriptome data files /scratch/7076164.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 13:08:47] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 13:16:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 13:26:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 13:36:42] Resuming TopHat pipeline with unmapped reads
[2019-06-26 13:36:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 13:46:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 13:47:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 13:49:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 13:58:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 13:59:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 14:01:18] Searching for junctions via segment mapping
[2019-06-26 14:06:06] Retrieving sequences for splices
[2019-06-26 14:08:31] Indexing splices
[2019-06-26 14:08:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 14:08:59] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 14:09:10] Joining segment hits
[2019-06-26 14:12:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 14:12:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 14:12:43] Joining segment hits
[2019-06-26 14:15:37] Reporting output tracks
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[2019-06-26 15:10:23] A summary of the alignment counts can be found in /scratch/7076164.1.linga/tophat2/align_summary.txt
[2019-06-26 15:10:23] Run complete: 02:17:57 elapsed