[2019-04-22 20:11:08] Beginning TopHat run (v2.1.1)
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[2019-04-22 20:11:08] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-22 20:11:08] Checking for Bowtie index files (genome)..
[2019-04-22 20:11:08] Checking for reference FASTA file
[2019-04-22 20:11:08] Generating SAM header for Bowtie2Index/genome
[2019-04-22 20:11:12] Reading known junctions from GTF file
[2019-04-22 20:11:16] Preparing reads
	 left reads: min. length=50, max. length=50, 9209331 kept reads (4203 discarded)
	right reads: min. length=50, max. length=50, 7769913 kept reads (1443621 discarded)
[2019-04-22 20:14:52] Building transcriptome data files /scratch/5525163.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-22 20:15:08] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-22 20:23:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:26:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:30:07] Resuming TopHat pipeline with unmapped reads
[2019-04-22 20:30:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 20:37:38] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 20:39:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 20:41:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 20:51:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 21:01:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 21:10:05] Searching for junctions via segment mapping
[2019-04-22 21:14:30] Retrieving sequences for splices
[2019-04-22 21:16:48] Indexing splices
[2019-04-22 21:17:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 21:17:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 21:18:06] Joining segment hits
[2019-04-22 21:21:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 21:21:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 21:22:56] Joining segment hits
[2019-04-22 21:26:16] Reporting output tracks
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[2019-04-22 22:02:14] A summary of the alignment counts can be found in /scratch/5525163.1.linga/tophat2/align_summary.txt
[2019-04-22 22:02:14] Run complete: 01:51:06 elapsed