[2019-04-29 16:40:02] Beginning TopHat run (v2.1.1)
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[2019-04-29 16:40:02] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 16:40:03] Checking for Bowtie index files (genome)..
[2019-04-29 16:40:03] Checking for reference FASTA file
[2019-04-29 16:40:03] Generating SAM header for Bowtie2Index/genome
[2019-04-29 16:40:05] Reading known junctions from GTF file
[2019-04-29 16:40:07] Preparing reads
	 left reads: min. length=35, max. length=43, 5115158 kept reads (22455 discarded)
	right reads: min. length=35, max. length=43, 5108329 kept reads (29284 discarded)
[2019-04-29 16:41:42] Building transcriptome data files /scratch/5765328.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 16:41:52] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 16:47:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 16:49:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 16:50:18] Resuming TopHat pipeline with unmapped reads
Warning: you have only one segment per read.
	If the read length is greater than or equal to 45bp,
	we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2019-04-29 16:50:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 16:51:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 16:51:37] Searching for junctions via segment mapping
[2019-04-29 16:52:42] Retrieving sequences for splices
[2019-04-29 16:53:47] Indexing splices
Building a SMALL index
[2019-04-29 16:53:59] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2019-04-29 16:54:01] Joining segment hits
[2019-04-29 16:55:39] Mapping right_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2019-04-29 16:55:41] Joining segment hits
[2019-04-29 16:57:15] Reporting output tracks
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[2019-04-29 17:01:02] A summary of the alignment counts can be found in /scratch/5765328.1.c/tophat2/align_summary.txt
[2019-04-29 17:01:02] Run complete: 00:21:00 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 4 files...