BFAST fasta2brg help

[Esther]

I'm trying to create a reference genome with BFAST using the inhouse reference genome. This file contains all the chromosomes of the human genome and is ~3 GB large. However, when I execute the following command:

bfast fasta2brg -f /../reference_human.fa -A 0

It gives the following error:


************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /../reference_human.fa.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /../reference_human.fa
space: [NT Space]
timing: [Not Using]
************************************************************
************************************************************
Reading from /../reference_human.fa.
Reading in [contig,pos]:
]-------1,----------0]Base:[
************************************************************
In function "RGBinaryRead": Fatal Error[OutOfRange]. Variable/Value: original.
Message: Not a valid base pair.
***** Exiting due to errors *****
************************************************************

When I run the chromosomes seperately the tool functiones fine. I can't find the source of the problem. What is going wrong here?

Is it possible to execute the run using multiple reference files? (Since the tool seems to work with a chromosome at a time)

[nilshomer]

I'm trying to create a reference genome with BFAST using the inhouse reference genome. This file contains all the chromosomes of the human genome and is ~3 GB large. However, when I execute the following command:

bfast fasta2brg -f /../reference_human.fa -A 0

It gives the following error:


************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /../reference_human.fa.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /../reference_human.fa
space: [NT Space]
timing: [Not Using]
************************************************************
************************************************************
Reading from /../reference_human.fa.
Reading in [contig,pos]:
]-------1,----------0]Base:[
************************************************************
In function "RGBinaryRead": Fatal Error[OutOfRange]. Variable/Value: original.
Message: Not a valid base pair.
***** Exiting due to errors *****
************************************************************

When I run the chromosomes seperately the tool functiones fine. I can't find the source of the problem. What is going wrong here?

Is it possible to execute the run using multiple reference files? (Since the tool seems to work with a chromosome at a time)

It looks like there may be an extra newline or carriage return in your reference. Are you running this on Windows or obtained the reference from a Windows machine? If so, you will have to run "dos2unix" on your reference.

[Esther]

Thank you, the dos2unix did the trick. The reference file was indeed created in Windows.

[kursuni]

Bfast fasta2brg -f filename

Hi,

I'm working on my thesis work and I'm trying to run BFAST software for aligning FASTQ datasets. I'm getting error written below. and the command is;
> bfast fasta2brg -f filename

The error is;
________________________________________________________________
****************
Checking input parameters supplied by the user ...
Validating fastaFileName SRR035022_1.filt.fastq.
Input arguments look good!
****************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: SRR035022_1.filt.fastq
space: [NT Space]
timing: [Not Using]
******************
Reading from SRR035022_1.filt.fastq.
********************
In function "RGBinaryRead": Fatal Error[OpenFileError]. Variable/Value: SRR035022_1.filt.fastq.
Message: Could not open file for reading.
The file stream error was:: Value too large for defined data type
***** Exiting due to errors *****
_____________________________________________________________


I couldnt figure out what the problem is...

Can you tell me what I'm doing wrong ?

Thanks in advance...

[nilshomer]

It looks like you are trying to create a binary reference from the read's fastq file. You should be using the reference FASTA file. See the manual (appendix) for a walk-through.