[2018-05-13 12:13:20] Beginning TopHat run (v2.1.1)
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[2018-05-13 12:13:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-05-13 12:13:21] Checking for Bowtie index files (genome)..
[2018-05-13 12:13:21] Checking for reference FASTA file
[2018-05-13 12:13:21] Generating SAM header for Bowtie2Index/genome
[2018-05-13 12:13:25] Reading known junctions from GTF file
[2018-05-13 12:13:29] Preparing reads
	 left reads: min. length=33, max. length=33, 24986872 kept reads (12231 discarded)
[2018-05-13 12:18:39] Building transcriptome data files /scratch/6184251.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-05-13 12:18:57] Building Bowtie index from RefSeq_GeneBody.fa
[2018-05-13 12:26:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-05-13 12:56:38] 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
[2018-05-13 12:56:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-05-13 13:03:27] Searching for junctions via segment mapping
[2018-05-13 13:05:27] Retrieving sequences for splices
[2018-05-13 13:07:36] Indexing splices
[2018-05-13 13:08:00] 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/6184251.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2018-05-13 13:08:04] Joining segment hits
[2018-05-13 13:16:46] Reporting output tracks
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[2018-05-13 13:30:23] A summary of the alignment counts can be found in /scratch/6184251.1.linga/tophat2/align_summary.txt
[2018-05-13 13:30:23] Run complete: 01:17:02 elapsed