[2019-04-28 08:03:47] Beginning TopHat run (v2.1.1)
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[2019-04-28 08:03:47] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-28 08:03:47] Checking for Bowtie index files (genome)..
[2019-04-28 08:03:47] Checking for reference FASTA file
[2019-04-28 08:03:47] Generating SAM header for Bowtie2Index/genome
[2019-04-28 08:03:49] Reading known junctions from GTF file
[2019-04-28 08:03:51] Preparing reads

WARNING: read pairing issues detected (check prep_reads.log) !

	 left reads: min. length=51, max. length=51, 59860546 kept reads (9650 discarded)
	right reads: min. length=51, max. length=51, 59866021 kept reads (4175 discarded)
[2019-04-28 08:24:22] Building transcriptome data files /scratch/5678641.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-04-28 08:24:31] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-28 08:29:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-28 09:00:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-28 09:31:55] Resuming TopHat pipeline with unmapped reads
[2019-04-28 09:31:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-28 09:35:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-28 09:36:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-28 09:36:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-28 09:40:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-28 09:41:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-28 09:42:25] Searching for junctions via segment mapping
[2019-04-28 09:48:17] Retrieving sequences for splices
[2019-04-28 09:49:18] Indexing splices
[2019-04-28 09:49:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-28 09:49:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-28 09:49:58] Joining segment hits
[2019-04-28 09:51:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-28 09:51:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-28 09:51:54] Joining segment hits
[2019-04-28 09:53:11] Reporting output tracks
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[2019-04-28 13:12:50] A summary of the alignment counts can be found in /scratch/5678641.1.p8/tophat2/align_summary.txt
[2019-04-28 13:12:50] Run complete: 05:09:03 elapsed