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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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ERROR: unexpected error during parser initialization #20

Closed foala closed 4 years ago

foala commented 4 years ago

Hi, I am new to raisd. I am using vcf filed generated by freebayes of a population of 50 (35 scaffolds) as an input. I get this error when I start running

ERROR: unexpected error during parser initialization

the command used is Command: ./RAiSD -n v2 -I ./input -f

please assist

alachins commented 4 years ago

This error appears when the file format is not recognized. Can you please send me the input file to look into that?

foala commented 4 years ago

Hi, Thank your for your prompt reply. It is a huge vcf file (25Gb).

foala commented 4 years ago

can you share with me a sample VCf file that works? to make sure its a format issue

alachins commented 4 years ago

Can you extract the first 50-100 lines? Which version are you using? The very first check for VCF files is that the file starts with the string: "##fileformat=VCF" Can you check this?

foala commented 4 years ago

Thank you for your reply here is the header from my VCF

fileformat=VCFv4.2

FILTER=

fileDate=20200606

source=freeBayes v1.3.2-dirty

reference=ref.fa

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

phasing=none

commandline="freebayes -L bam.txt -@ filtered20.vcf.gz -l --region=scaffold_1|arrow:1-126869364 -f ref.fa"

filter="QUAL > 20"

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

alachins commented 4 years ago

I just put these lines in a txt file and RAiSD v2.8 (the latest) identifies that it is a vcf header. So the parser is correctly initialized.

alachins commented 4 years ago

That's very strange. I can check it in more detail if you can send me an input file, no matter how small, as long as it generates the error. n.alachiotis@gmail.com

foala commented 4 years ago

Thank you very much for your help. I will keep you posted, and will close this thread for now