Comments (4)
Dear shiyi-pan, just to check do you have the latest version? The "hts_internal" problem was fixed a few days ago. Could you run the following:
make clean
git status
git pull origin master
make
Could you paste the contents of:
.git/logs/HEAD
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thank you ,grenaud . I downloaded the latest version and compiled the software. But I got a new error when I run it. I hope you can do me a favour.
I have two problem. first , when I run it in command line,my command is that:
glactools vcf2acf --fai Gmax_275_v2.0.fa.fai --onlyGT Z-001.recode.vcf Z-001 > a.acf.gz
but I got a warning like that :
Warning: if several sites are rejected due to being empty, it could be due to the absence of the PL field, please rerun using the onlyGT flag.
Program terminated gracefully.
I have already used the onlyGT flag. I don't know why and here is my vcf file:
##fileformat=VCFv4.2
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Z-001
1 4485 Chr01_4485 G A . . . GT 1/1
1 5564 Chr01_5564 C T . . . GT 0/0
1 5698 Chr01_5698 C T . . . GT 0/0
1 5899 Chr01_5899 T C . . . GT 1/1
the seconded problem. when I run it in a script , It don't have a result. my script is like that:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -l mem_free=4G
VCFTOOLS=/share/apps/vcftools/vcftools-0.1.15
GLACTOOLS=/ds3512/home/panyp/ruanjian/glactools/
SAMTOOLS=/ds3512/home/panyp/ruanjian/samtools-1.9/bin
DIR=/ds3512/home/panyp/diff_genome/
$SAMTOOLS/samtools faidx $DIR/Gmax_275_v2.0.fa
$VCFTOOLS --vcf chr01.recode.vcf --indv Z-001 --out Z-001 --recode
$GLACTOOLS/glactools vcf2acf --fai $DIR/Gmax_275_v2.0.fa.fai --onlyGT Z-001.recode.vcf Z-001 > Z-001.acf.gz
Z-001 is my sample ID. It generate a 'Z-001.acf.gz' file but the file can't be decompressed :
gzip: Z-001.acf.gz: unexpected end of file.
I check the log and find that:
Filter used: Cutoffs :
Minimum genotype quality (GQ) = 0
Minimum RMS of the mapping qualities (MQ) = 0
Minimum mapability = 0
Filter sites close to an indel = currently turned on/used
Filter sites close labeled as repeat masked (RM) = currently turned on/used
Filter sites close labeled as systematic error (SysErr) = currently turned on/used
Minimum coverage = 0
Minimum coverage = 1000
Cannot write to /dev/stdout.
from glactools.
great! Would you mind that we close this issue and could you open a new one?
from glactools.
thank you,you can close this one .
from glactools.
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