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Old 06-16-2011, 06:41 AM   #1
Location: new york

Join Date: Jun 2011
Posts: 23
Default Tophat and SOLID -> zero kb .bed files


I'm somewhat relatively new in the NGS data analysis though i've been reading and searching a lot for the last couple of months. I've recently got a new computer to do my own analysis and set up Tophat to run before i left work last night. I came into work to find this error message on terminal:

[Wed Jun 15 17:27:11 2011] Beginning TopHat run (v1.3.0)
[Wed Jun 15 17:27:11 2011] Preparing output location ./tophat_out/
[Wed Jun 15 17:27:11 2011] Checking for Bowtie index files
[Wed Jun 15 17:27:11 2011] Checking for reference FASTA file
	Warning: Could not find FASTA file /usr/local/indexes/hg19_c.fa
[Wed Jun 15 17:27:11 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/local/bowtie-inspect /usr/local/indexes/hg19_c > ./tophat_out/tmp/hg19_c.fa
[Wed Jun 15 17:30:39 2011] Checking for Bowtie
	Bowtie version:
[Wed Jun 15 17:30:39 2011] Checking for Samtools
	Samtools Version: 0.1.16
[Wed Jun 15 17:30:39 2011] Generating SAM header for /usr/local/indexes/hg19_c
[Wed Jun 15 17:31:02 2011] Preparing reads
	format:		 fasta
	Left  reads: min. length=51, count=110342407
[Wed Jun 15 18:10:02 2011] Mapping left_kept_reads against hg19_c with Bowtie 
[Wed Jun 15 19:13:38 2011] Processing bowtie hits
[Wed Jun 15 20:41:53 2011] Mapping left_kept_reads_seg1 against hg19_c with Bowtie (1/2)
[Wed Jun 15 21:38:25 2011] Mapping left_kept_reads_seg2 against hg19_c with Bowtie (2/2)
[Wed Jun 15 22:21:20 2011] Searching for junctions via segment mapping
[Wed Jun 15 23:13:44 2011] Retrieving sequences for splices
[Wed Jun 15 23:19:01 2011] Indexing splices
[Wed Jun 15 23:19:03 2011] Mapping left_kept_reads_seg1 against segment_juncs with Bowtie (1/2)
[Wed Jun 15 23:23:37 2011] Mapping left_kept_reads_seg2 against segment_juncs with Bowtie (2/2)
[Wed Jun 15 23:28:10 2011] Joining segment hits
[Thu Jun 16 00:02:51 2011] Reporting output tracks
Error: [Errno 2] No such file or directory
[samopen] SAM header is present: 25 sequences.
Seems like everything ran quite nicely but something failed and all the .bed files Tophat output are all 0kb. I tried searching google but couldn't find information related to this error. Any idea what this is?
ahmetz is offline   Reply With Quote
Old 06-16-2011, 01:04 PM   #2
Junior Member
Location: sd

Join Date: Jun 2011
Posts: 4

I meet the same issue. one of output files (accepted_hits.bam ) was not created
dong01 is offline   Reply With Quote

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