[2019-06-24 21:37:05] Beginning TopHat run (v2.1.1)
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[2019-06-24 21:37:05] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 21:37:05] Checking for Bowtie index files (genome)..
[2019-06-24 21:37:05] Checking for reference FASTA file
[2019-06-24 21:37:05] Generating SAM header for Bowtie2Index/genome
[2019-06-24 21:37:06] Reading known junctions from GTF file
[2019-06-24 21:37:08] Preparing reads
	 left reads: min. length=32, max. length=36, 24145578 kept reads (44096 discarded)
	right reads: min. length=32, max. length=36, 23847178 kept reads (342496 discarded)
[2019-06-24 21:42:53] Building transcriptome data files /scratch/7056805.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 21:43:02] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 21:47:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:52:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:57:45] 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 21:57:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 21:58:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:01:57] Searching for junctions via segment mapping
[2019-06-24 22:03:07] Retrieving sequences for splices
[2019-06-24 22:04:20] Indexing splices
[2019-06-24 22:04:27] 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/7056805.1.c/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:04:29] Joining segment hits
[2019-06-24 22:07:12] 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/7056805.1.c/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:07:14] Joining segment hits
[2019-06-24 22:09:58] Reporting output tracks
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[2019-06-24 22:24:01] A summary of the alignment counts can be found in /scratch/7056805.1.c/tophat2/align_summary.txt
[2019-06-24 22:24:01] Run complete: 00:46:56 elapsed