[2019-04-28 08:02:03] Beginning TopHat run (v2.1.1)
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[2019-04-28 08:02:03] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-28 08:02:03] Checking for Bowtie index files (genome)..
[2019-04-28 08:02:03] Checking for reference FASTA file
[2019-04-28 08:02:03] Generating SAM header for Bowtie2Index/genome
[2019-04-28 08:02:05] Reading known junctions from GTF file
[2019-04-28 08:02:08] Preparing reads

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

	 left reads: min. length=51, max. length=51, 55579048 kept reads (10698 discarded)
	right reads: min. length=51, max. length=51, 55584230 kept reads (5516 discarded)
[2019-04-28 08:21:39] Building transcriptome data files /scratch/5678640.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-04-28 08:21:51] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-28 08:27:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-28 08:58:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-28 09:31:18] Resuming TopHat pipeline with unmapped reads
[2019-04-28 09:31:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-28 09:35:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-28 09:36:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-28 09:36:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-28 09:41:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-28 09:41:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-28 09:43:11] Searching for junctions via segment mapping
[2019-04-28 09:49:41] Retrieving sequences for splices
[2019-04-28 09:50:48] Indexing splices
[2019-04-28 09:51:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-28 09:51:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-28 09:51:30] Joining segment hits
[2019-04-28 09:52:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-28 09:53:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-28 09:53:38] Joining segment hits
[2019-04-28 09:55:04] Reporting output tracks
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[2019-04-28 13:11:24] A summary of the alignment counts can be found in /scratch/5678640.1.c/tophat2/align_summary.txt
[2019-04-28 13:11:24] Run complete: 05:09:21 elapsed