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Old 06-11-2010, 09:00 AM   #1
zhanxw
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Location: umich

Join Date: Jun 2009
Posts: 7
Default BFAST index, not understand warnings

Hello,

I want to created index files in color space from NCBI build 36 in color space.
Here is my command
`which time` bfast index -f NCBI36.fa -n 8 -w 14 -i 1 -A 1 -m 1111111111111111111111

Then I got warning like "startContig was less than zero.", "endContig was greater than the number of contigs in the reference genome.". But I am sure I am using the same FASTA reference genome file. So is there anything I should do for these warnings? And is anyone have experience about how long it takes to build this index file?

Part of the outputs:
------------------------------------------------------
Checking input parameters supplied by the user ...
Validating fastaFileName NCBI36.fa.
Validating tmpDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: NCBI36.fa
space: [Color Space]
mask: 1111111111111111111111
depth: 0
hashWidth: 14
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 NCBI36.fa.cs.brg.
In total read 23 contigs for a total of 3022646526 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=23 and position=154913754.
************************************************************
Currently on [contig,pos]:
[-------4,---27000000]

------------------------------------------------------
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Old 06-11-2010, 09:14 AM   #2
nilshomer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by zhanxw View Post
Hello,

I want to created index files in color space from NCBI build 36 in color space.
Here is my command
`which time` bfast index -f NCBI36.fa -n 8 -w 14 -i 1 -A 1 -m 1111111111111111111111

Then I got warning like "startContig was less than zero.", "endContig was greater than the number of contigs in the reference genome.". But I am sure I am using the same FASTA reference genome file. So is there anything I should do for these warnings? And is anyone have experience about how long it takes to build this index file?

Part of the outputs:
------------------------------------------------------
Checking input parameters supplied by the user ...
Validating fastaFileName NCBI36.fa.
Validating tmpDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: NCBI36.fa
space: [Color Space]
mask: 1111111111111111111111
depth: 0
hashWidth: 14
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 NCBI36.fa.cs.brg.
In total read 23 contigs for a total of 3022646526 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=23 and position=154913754.
************************************************************
Currently on [contig,pos]:
[-------4,---27000000]

------------------------------------------------------
You can ignore the warnings if you didn't specify the "-s" or "-e" options. Each index takes about 4-5 hours to build (8 threads).
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