[2019-04-29 17:21:15] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:21:15] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:21:15] Checking for Bowtie index files (genome)..
[2019-04-29 17:21:15] Checking for reference FASTA file
[2019-04-29 17:21:15] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:21:17] Reading known junctions from GTF file
[2019-04-29 17:21:19] Preparing reads
	 left reads: min. length=35, max. length=43, 5127420 kept reads (20808 discarded)
	right reads: min. length=35, max. length=43, 5121124 kept reads (27104 discarded)
[2019-04-29 17:22:55] Building transcriptome data files /scratch/5765357.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:23:04] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:27:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:29:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:30:43] 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 17:30:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:31:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:31:54] Searching for junctions via segment mapping
[2019-04-29 17:32:53] Retrieving sequences for splices
[2019-04-29 17:33:53] Indexing splices
Building a SMALL index
[2019-04-29 17:34:04] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2019-04-29 17:34:06] Joining segment hits
[2019-04-29 17:35:35] Mapping right_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2019-04-29 17:35:36] Joining segment hits
[2019-04-29 17:37:01] Reporting output tracks
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[2019-04-29 17:40:40] A summary of the alignment counts can be found in /scratch/5765357.1.p/tophat2/align_summary.txt
[2019-04-29 17:40:40] Run complete: 00:19:25 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 4 files...