[2019-06-24 22:00:33] Beginning TopHat run (v2.1.1)
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[2019-06-24 22:00:33] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 22:00:33] Checking for Bowtie index files (genome)..
[2019-06-24 22:00:33] Checking for reference FASTA file
[2019-06-24 22:00:33] Generating SAM header for Bowtie2Index/genome
[2019-06-24 22:00:35] Reading known junctions from GTF file
[2019-06-24 22:00:36] Preparing reads
	 left reads: min. length=32, max. length=36, 18042185 kept reads (45969 discarded)
	right reads: min. length=32, max. length=36, 17936885 kept reads (151269 discarded)
[2019-06-24 22:04:45] Building transcriptome data files /scratch/7056810.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 22:04:54] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 22:09:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 22:13:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 22:17:26] 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
[2019-06-24 22:17:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:18:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:19:33] Searching for junctions via segment mapping
[2019-06-24 22:20:40] Retrieving sequences for splices
[2019-06-24 22:21:49] Indexing splices
[2019-06-24 22:21:55] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
open: No such file or directory
Error: bam2fastx failed to open BAM file /scratch/7056810.1.p8/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:21:57] Joining segment hits
[2019-06-24 22:23:59] Mapping right_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
open: No such file or directory
Error: bam2fastx failed to open BAM file /scratch/7056810.1.p8/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:24:00] Joining segment hits
[2019-06-24 22:26:05] Reporting output tracks
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[2019-06-24 22:39:01] A summary of the alignment counts can be found in /scratch/7056810.1.p8/tophat2/align_summary.txt
[2019-06-24 22:39:01] Run complete: 00:38:28 elapsed