[2018-05-07 05:38:04] Beginning TopHat run (v2.0.8)
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[2018-05-07 05:38:04] Checking for Bowtie
		  Bowtie version:	 0.12.9.0
[2018-05-07 05:38:04] Checking for Samtools
		Samtools version:	 0.1.19.0
[2018-05-07 05:38:04] Checking for Bowtie index files
[2018-05-07 05:38:04] Checking for Bowtie index files
[2018-05-07 05:38:04] Checking for reference FASTA file
[2018-05-07 05:38:04] Generating SAM header for /oak/stanford/groups/akundaje/marinovg/genomes/dm6/bowtie-indexes/dm6
	format:		 fastq
	quality scale:	 phred33 (default)
[2018-05-07 05:38:05] Reading known junctions from GTF file
[2018-05-07 05:38:09] Preparing reads
	 left reads: min. length=36, max. length=36, 4077336 kept reads (1373 discarded)
[2018-05-07 05:38:39] Using pre-built transcriptome index..
[2018-05-07 05:38:42] Mapping left_kept_reads to transcriptome Drosophila_melanogaster.BDGP6.90 with Bowtie 
[2018-05-07 05:39:44] 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
[2018-05-07 05:39:44] Mapping left_kept_reads.m2g_um to genome dm6 with Bowtie 
[2018-05-07 05:40:47] Searching for junctions via segment mapping
[2018-05-07 05:41:17] Retrieving sequences for splices
[2018-05-07 05:41:22] Indexing splices
[2018-05-07 05:41:32] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie (1/1)
open: No such file or directory
Error: bam2fastx failed to open BAM file S2-CAGE-Rep1-Celniker-ENCFF988NQG-TopHat-2.0.8/tmp/left_kept_reads.m2g_um_unmapped.bam
[2018-05-07 05:41:36] Joining segment hits
[2018-05-07 05:41:49] Reporting output tracks
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[2018-05-07 05:42:27] Run complete: 00:04:23 elapsed