[2018-05-13 12:13:55] Beginning TopHat run (v2.1.1)
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[2018-05-13 12:13:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-05-13 12:13:55] Checking for Bowtie index files (genome)..
[2018-05-13 12:13:55] Checking for reference FASTA file
[2018-05-13 12:13:55] Generating SAM header for Bowtie2Index/genome
[2018-05-13 12:14:02] Reading known junctions from GTF file
[2018-05-13 12:14:06] Preparing reads
	 left reads: min. length=33, max. length=33, 17155514 kept reads (7998 discarded)
[2018-05-13 12:17:58] Building transcriptome data files /scratch/6184256.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-05-13 12:18:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-05-13 12:34:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-05-13 13:03:58] 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 13:03:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-05-13 13:10:52] Searching for junctions via segment mapping
[2018-05-13 13:13:59] Retrieving sequences for splices
[2018-05-13 13:16:47] Indexing splices
[2018-05-13 13:17:14] 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/6184256.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2018-05-13 13:17:18] Joining segment hits
[2018-05-13 13:25:41] Reporting output tracks
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[2018-05-13 13:39:53] A summary of the alignment counts can be found in /scratch/6184256.1.linga/tophat2/align_summary.txt
[2018-05-13 13:39:53] Run complete: 01:25:57 elapsed