[2019-04-28 07:58:59] Beginning TopHat run (v2.1.1)
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[2019-04-28 07:58:59] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-28 07:58:59] Checking for Bowtie index files (genome)..
[2019-04-28 07:58:59] Checking for reference FASTA file
[2019-04-28 07:58:59] Generating SAM header for Bowtie2Index/genome
[2019-04-28 07:59:01] Reading known junctions from GTF file
[2019-04-28 07:59:04] Preparing reads

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

	 left reads: min. length=51, max. length=51, 69282885 kept reads (18412 discarded)
	right reads: min. length=51, max. length=51, 69293827 kept reads (7470 discarded)
[2019-04-28 08:22:30] Building transcriptome data files /scratch/5678638.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-04-28 08:22:39] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-28 08:27:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-28 09:12:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-28 09:58:37] Resuming TopHat pipeline with unmapped reads
[2019-04-28 09:58:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-28 10:03:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-28 10:03:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-28 10:04:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-28 10:09:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-28 10:10:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-28 10:11:19] Searching for junctions via segment mapping
[2019-04-28 10:18:53] Retrieving sequences for splices
[2019-04-28 10:19:53] Indexing splices
[2019-04-28 10:20:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-28 10:20:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-28 10:20:46] Joining segment hits
[2019-04-28 10:22:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-28 10:22:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-28 10:22:59] Joining segment hits
[2019-04-28 10:24:22] Reporting output tracks
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[2019-04-28 15:58:08] A summary of the alignment counts can be found in /scratch/5678638.1.p/tophat2/align_summary.txt
[2019-04-28 15:58:08] Run complete: 07:59:09 elapsed