[2019-05-08 08:30:37] Beginning TopHat run (v2.1.1)
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[2019-05-08 08:30:37] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 08:30:37] Checking for Bowtie index files (genome)..
[2019-05-08 08:30:37] Checking for reference FASTA file
[2019-05-08 08:30:37] Generating SAM header for Bowtie2Index/genome
[2019-05-08 08:30:40] Reading known junctions from GTF file
[2019-05-08 08:30:42] Preparing reads
	 left reads: min. length=101, max. length=101, 34562887 kept reads (242363 discarded)
[2019-05-08 08:39:33] Building transcriptome data files /scratch/5992723.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 08:39:42] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 08:44:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 08:56:18] Resuming TopHat pipeline with unmapped reads
[2019-05-08 08:56:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 09:02:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 09:03:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 09:04:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 09:05:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 09:05:57] Searching for junctions via segment mapping
[2019-05-08 09:12:25] Retrieving sequences for splices
[2019-05-08 09:13:32] Indexing splices
[2019-05-08 09:14:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 09:14:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 09:14:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 09:14:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 09:15:11] Joining segment hits
[2019-05-08 09:16:52] Reporting output tracks
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[2019-05-08 09:29:51] A summary of the alignment counts can be found in /scratch/5992723.1.p16/tophat2/align_summary.txt
[2019-05-08 09:29:51] Run complete: 00:59:14 elapsed