[2019-06-24 20:54:58] Beginning TopHat run (v2.1.1)
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[2019-06-24 20:54:58] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 20:54:58] Checking for Bowtie index files (genome)..
[2019-06-24 20:54:58] Checking for reference FASTA file
[2019-06-24 20:54:58] Generating SAM header for Bowtie2Index/genome
[2019-06-24 20:55:00] Reading known junctions from GTF file
[2019-06-24 20:55:02] Preparing reads
	 left reads: min. length=32, max. length=36, 22083167 kept reads (52972 discarded)
	right reads: min. length=32, max. length=36, 21860410 kept reads (275729 discarded)
[2019-06-24 21:00:04] Building transcriptome data files /scratch/7056801.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 21:00:13] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 21:04:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:08:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:13:26] 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 21:13:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 21:14:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 21:16:54] Searching for junctions via segment mapping
[2019-06-24 21:18:01] Retrieving sequences for splices
[2019-06-24 21:19:09] Indexing splices
[2019-06-24 21:19:16] 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/7056801.1.p8/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 21:19:17] Joining segment hits
[2019-06-24 21:21:50] 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/7056801.1.p8/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 21:21:52] Joining segment hits
[2019-06-24 21:24:28] Reporting output tracks
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[2019-06-24 21:37:48] A summary of the alignment counts can be found in /scratch/7056801.1.p8/tophat2/align_summary.txt
[2019-06-24 21:37:48] Run complete: 00:42:50 elapsed