[2019-06-24 19:46:28] Beginning TopHat run (v2.1.1)
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[2019-06-24 19:46:28] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 19:46:28] Checking for Bowtie index files (genome)..
[2019-06-24 19:46:28] Checking for reference FASTA file
[2019-06-24 19:46:28] Generating SAM header for Bowtie2Index/genome
[2019-06-24 19:46:30] Reading known junctions from GTF file
[2019-06-24 19:46:32] Preparing reads
	 left reads: min. length=32, max. length=36, 22942893 kept reads (56938 discarded)
	right reads: min. length=32, max. length=36, 22605116 kept reads (394715 discarded)
[2019-06-24 19:51:48] Building transcriptome data files /scratch/7056798.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 19:51:56] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 19:56:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 20:00:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 20:05:17] 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 20:05:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:06:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:09:36] Searching for junctions via segment mapping
[2019-06-24 20:10:43] Retrieving sequences for splices
[2019-06-24 20:11:52] Indexing splices
[2019-06-24 20:11:58] 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/7056798.1.p8/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:12:00] Joining segment hits
[2019-06-24 20:14:45] 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/7056798.1.p8/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:14:47] Joining segment hits
[2019-06-24 20:17:31] Reporting output tracks
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[2019-06-24 20:31:09] A summary of the alignment counts can be found in /scratch/7056798.1.p8/tophat2/align_summary.txt
[2019-06-24 20:31:09] Run complete: 00:44:40 elapsed