[2019-04-28 08:01:10] Beginning TopHat run (v2.1.1)
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[2019-04-28 08:01:10] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-28 08:01:11] Checking for Bowtie index files (genome)..
[2019-04-28 08:01:11] Checking for reference FASTA file
[2019-04-28 08:01:11] Generating SAM header for Bowtie2Index/genome
[2019-04-28 08:01:16] Reading known junctions from GTF file
[2019-04-28 08:01:21] Preparing reads

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

	 left reads: min. length=51, max. length=51, 55643421 kept reads (10154 discarded)
	right reads: min. length=51, max. length=51, 55649146 kept reads (4429 discarded)
[2019-04-28 08:52:07] Building transcriptome data files /scratch/5678639.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-28 08:52:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-28 09:04:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-28 12:27:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-28 15:43:03] Resuming TopHat pipeline with unmapped reads
[2019-04-28 15:43:03] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-28 15:56:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-28 15:58:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-28 16:01:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-28 16:13:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-28 16:16:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-28 16:19:30] Searching for junctions via segment mapping
[2019-04-28 16:39:52] Retrieving sequences for splices
[2019-04-28 16:43:08] Indexing splices
[2019-04-28 16:43:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-28 16:44:58] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-28 16:46:19] Joining segment hits
[2019-04-28 16:50:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-28 16:51:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-28 16:53:35] Joining segment hits
[2019-04-28 16:57:14] Reporting output tracks
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[2019-04-29 05:14:04] A summary of the alignment counts can be found in /scratch/5678639.1.linga/tophat2/align_summary.txt
[2019-04-29 05:14:04] Run complete: 21:12:53 elapsed