[2019-04-29 17:22:22] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:22:22] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:22:22] Checking for Bowtie index files (genome)..
[2019-04-29 17:22:22] Checking for reference FASTA file
[2019-04-29 17:22:22] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:22:25] Reading known junctions from GTF file
[2019-04-29 17:22:27] Preparing reads
	 left reads: min. length=35, max. length=43, 5200759 kept reads (23990 discarded)
	right reads: min. length=35, max. length=43, 5198684 kept reads (26065 discarded)
[2019-04-29 17:24:04] Building transcriptome data files /scratch/5765358.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:24:12] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:29:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:30:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:31:51] 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 17:31:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:32:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:33:04] Searching for junctions via segment mapping
[2019-04-29 17:34:02] Retrieving sequences for splices
[2019-04-29 17:35:02] Indexing splices
Building a SMALL index
[2019-04-29 17:35:14] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2019-04-29 17:35:16] Joining segment hits
[2019-04-29 17:36:44] Mapping right_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2019-04-29 17:36:46] Joining segment hits
[2019-04-29 17:38:10] Reporting output tracks
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[2019-04-29 17:41:53] A summary of the alignment counts can be found in /scratch/5765358.1.p/tophat2/align_summary.txt
[2019-04-29 17:41:53] Run complete: 00:19:30 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 4 files...