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Old 05-23-2013, 03:18 PM   #1
robertthebob1
Junior Member
 
Location: Bethesda, MD

Join Date: May 2013
Posts: 2
Default BFAST, Could not read in buffer

I'm having some problem getting started with Bfast:
bob@homequad:/home2/NGS/tmp$ bfast index -n 8 -f /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta -m 111111111111111111 -w 18 -i 1
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta.
Validating tmpDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta
space: [NT Space]
mask: 111111111111111111
depth: 0
hashWidth: 18
indexNumber: 1
repeatMasker: [Not Using]
startContig: 0
startPos: 0
endContig: 2147483647
endPos: 2147483647
exonsFileName: [Not Using]
numThreads: 8
tmpDir: ./
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from /home2/NGS/ref/yeast/seq/S288C_reference_sequence_R64-1-1_20110203.fasta.nt.brg.
In total read 17 contigs for a total of 12157105 bases
************************************************************
Creating the index...
************************************************************
Warning: startContig was less than zero.
Defaulting to contig=1 and position=1.
************************************************************
************************************************************
Warning: endContig was greater than the number of contigs in the reference genome.
Defaulting to reference genome's end contig=17 and position=85779.
************************************************************
Currently on [contig,pos]:
[------17,------85779]
Sorting by thread...
24.998 percent complete************************************************************
In function "RGIndexMergeHelperFromDiskGetNext_8": Fatal Error[ReadFileError]. Message: Could not read in buffer.
The file stream error was:: Bad file descriptor
***** Exiting due to errors *****
************************************************************
bob@homequad:/home2/NGS/tmp$

I've looked at the source and can't see right away what the problem
might be. May I ask for Nils' help?
Robert Williams
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