[2019-06-24 21:19:30] Beginning TopHat run (v2.1.1)
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[2019-06-24 21:19:30] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 21:19:30] Checking for Bowtie index files (genome)..
[2019-06-24 21:19:30] Checking for reference FASTA file
[2019-06-24 21:19:30] Generating SAM header for Bowtie2Index/genome
[2019-06-24 21:19:35] Reading known junctions from GTF file
[2019-06-24 21:19:38] Preparing reads
	 left reads: min. length=32, max. length=36, 22773669 kept reads (33842 discarded)
	right reads: min. length=32, max. length=36, 22640595 kept reads (166916 discarded)
[2019-06-24 21:29:21] Building transcriptome data files /scratch/7056803.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 21:29:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 21:36:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:47:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:58:12] 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 21:58:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:00:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:04:09] Searching for junctions via segment mapping
[2019-06-24 22:06:28] Retrieving sequences for splices
[2019-06-24 22:08:37] Indexing splices
[2019-06-24 22:08:50] 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/7056803.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:08:53] Joining segment hits
[2019-06-24 22:14:58] 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/7056803.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:15:01] Joining segment hits
[2019-06-24 22:21:25] Reporting output tracks
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[2019-06-24 23:15:28] A summary of the alignment counts can be found in /scratch/7056803.1.linga/tophat2/align_summary.txt
[2019-06-24 23:15:28] Run complete: 01:55:58 elapsed