[2019-05-08 08:31:10] Beginning TopHat run (v2.1.1)
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[2019-05-08 08:31:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 08:31:11] Checking for Bowtie index files (genome)..
[2019-05-08 08:31:11] Checking for reference FASTA file
[2019-05-08 08:31:11] Generating SAM header for Bowtie2Index/genome
[2019-05-08 08:31:13] Reading known junctions from GTF file
[2019-05-08 08:31:16] Preparing reads
	 left reads: min. length=101, max. length=101, 32565514 kept reads (254086 discarded)
[2019-05-08 08:39:53] Building transcriptome data files /scratch/5992724.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 08:40:03] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 08:45:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 09:00:50] Resuming TopHat pipeline with unmapped reads
[2019-05-08 09:00:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 09:06:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 09:07:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 09:08:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 09:08:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 09:09:33] Searching for junctions via segment mapping
[2019-05-08 09:22:11] Retrieving sequences for splices
[2019-05-08 09:23:25] Indexing splices
[2019-05-08 09:24:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 09:24:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 09:25:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 09:25:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 09:25:53] Joining segment hits
[2019-05-08 09:27:43] Reporting output tracks
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[2019-05-08 09:41:07] A summary of the alignment counts can be found in /scratch/5992724.1.c/tophat2/align_summary.txt
[2019-05-08 09:41:07] Run complete: 01:09:56 elapsed