[2019-06-24 22:56:38] Beginning TopHat run (v2.1.1)
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[2019-06-24 22:56:38] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 22:56:38] Checking for Bowtie index files (genome)..
[2019-06-24 22:56:38] Checking for reference FASTA file
[2019-06-24 22:56:38] Generating SAM header for Bowtie2Index/genome
[2019-06-24 22:56:40] Reading known junctions from GTF file
[2019-06-24 22:56:42] Preparing reads
	 left reads: min. length=32, max. length=36, 18147441 kept reads (115459 discarded)
	right reads: min. length=32, max. length=36, 17941404 kept reads (321496 discarded)
[2019-06-24 23:00:50] Building transcriptome data files /scratch/7056815.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 23:01:00] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 23:05:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 23:09:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 23:13:00] 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 23:13:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 23:13:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 23:16:09] Searching for junctions via segment mapping
[2019-06-24 23:17:17] Retrieving sequences for splices
[2019-06-24 23:18:26] Indexing splices
[2019-06-24 23:18:33] 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/7056815.1.p/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 23:18:35] Joining segment hits
[2019-06-24 23:20:37] 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/7056815.1.p/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 23:20:38] Joining segment hits
[2019-06-24 23:22:40] Reporting output tracks
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[2019-06-24 23:32:36] A summary of the alignment counts can be found in /scratch/7056815.1.p/tophat2/align_summary.txt
[2019-06-24 23:32:36] Run complete: 00:35:58 elapsed