Ok let's do this one problem at a time. The first, your command:
glactools vcf2acf --fai Gmax_275_v2.0.fa.fai --onlyGT Z-001.recode.vcf Z-001 > a.acf.gz

Could you post the .fai file and the vcf file to a dropbox or something and please send me the link? I will have a look.

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grenaud:
Thank you for your help.I have upload my file in appendix. The file is big so that I upload a part of it.
glactools_file.zip
when I install the glactools,some warning happended like that:

my GCC version is 8.3. and cmake is 3.5.2 .
I also met a error like but when I type 'make' again, It when through whithout the error so I ignore it . I think maybe it's the reason why I'can get the right result.
sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 /ds3512/home/panyp/ruanjian/xz/lib/liblzma.so -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp
sed: -e expression #1, char 47: unknown option to `s'
make[1]: *** [htslib.pc.tmp] Error 1.

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Regarding the warnings, they are just warnings. I have on my todo list to take care of them.

I tried unzipping the file and I get:
unzip glactools_file.zip
Archive: glactools_file.zip
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.

could you post a bit of the vcf in zipped to a dropbox/link and the fasta index?

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ok，I try to upload it again.
chr01.zip

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Dear shiyi-pan, sorry for the late reply! I found a minor bug where it filtered out sites based on coverage even if there was no coverage. I have since fixed it. BTW, in the example you sent I noticed a discrepancy between the chromosome name used in the VCF file ('1') and the one in the fasta file ('Chr01'). You should use the exact fasta file used for mapping as to avoid any problems. Let me know if that works for you if so I will close this issue.

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thank you,grenaud ，I downloaded the latest version of glactools and installed it, when I run the 'vcf2acf' in command line ,it still print like 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

rejectIndel 0
rejectREFValidREF 0
rejectREFValidALT 0
rejectLOWCOV_REF 0
rejectMap20 0
rejectLOWMQ 0
rejectLOWQUAL 0
rejectCloseIndels 0
rejectSysERR 0
rejectRM 0
rejectREF_unknownGeno 0
rejectedEMPTY 0
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.

is that normal?

when I run it in script, it also didn't get a result. the log is here :

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.

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I ran the program with the following command on your data:
glactools vcf2acf --fai chr01/Chr01.fa.fai --onlyGT chr01/chr01.recode.vcf Z-001 > a.acf.gz

It returned a file:
glactools view -h a.acf.gz|head #chr coord REF,ALT root anc Z-001 1 4485 G,A 0,0:0 0,0:0 0,2:0 1 5564 C,N 0,0:0 0,0:0 2,0:0 1 5698 C,N 0,0:0 0,0:0 2,0:0 1 5899 T,C 0,0:0 0,0:0 0,2:0 1 6035 G,A 0,0:0 0,0:0 0,2:0 1 6324 C,N 0,0:0 0,0:0 2,0:0 1 6333 C,N 0,0:0 0,0:0 2,0:0 1 6443 A,G 0,0:0 0,0:0 0,2:0 1 6474 C,N 0,0:0 0,0:0 2,0:0

which command did you use?

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thank you for your attention,grenaud. I run the same command as yours and madifid the chromosome name in VCF file. I can get the same result like yours in command line,but I'm not sure it correct because the log end with that:

Program terminated gracefully

when I run the same command in my shell script, it told my 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
Error: GlacParser tried to read 4 bytes but got 0.

Here is my shell script:

#!/bin/bash

#$ -cwd
#$ -j y
#$ -S /bin/bash

#$ -l mem_free=4G

export PATH=/ds3512/home/panyp/denovo/gcc-8.3/bin:$PATH
export PATH=/ds3512/home/panyp/denovo/gcc-8.3/lib64:$PATH
export LD_LIBRARY_PATH=/ds3512/home/panyp/denovo/gcc-8.3/lib64/:$LD_LIBRARY_PATH

export PATH=/ds3512/home/panyp/ruanjian/xz/bin:$PATH
export LD_LIBRARY_PATH=/ds3512/home/panyp/ruanjian/xz/lib:$LD_LIBRARY_PATH
export LDFLAGS="-L/ds3512/home/panyp/ruanjian/xz/lib"
export CFLAGS="-I/ds3512/home/panyp/ruanjian/xz/include"

VCFTOOLS=/share/apps/vcftools/vcftools-0.1.15
GLACTOOLS=/ds3512/home/panyp/750cexu/balance_selection/glactools-master
SAMTOOLS=/ds3512/home/panyp/ruanjian/samtools-1.9/bin
PYTHON=/ds3512/home/panyp/ruanjian/python36/bin/python

DIR=/ds3512/home/panyp/diff_genome/

$SAMTOOLS/samtools faidx Chr01.fa

$VCFTOOLS --vcf chr01.recode.vcf --indv Z-001 --out Z-001 --recode

$PYTHON vcf_modify.py Z-001.recode.vcf > final-Z-001.recode.vcf
$GLACTOOLS/glactools vcf2acf --fai Chr01.fa.fai --onlyGT final-Z-001.recode.vcf Z-001 > b.acf.gz
$GLACTOOLS/glactools view -h b.acf.gz|tail

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Could you try to run the commands outside the shell script? Because with this, we do not know which command fails.

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ok,here is my commands in command line and I can get the "a.acf.gz" file:

/ds3512/home/panyp/750cexu/balance_selection/glactools-master/glactools vcf2acf --fai Chr01.fa.fai --onlyGT final-Z-001.recode.vcf Z-001 > a.acf.gz

but I still got some log on my screen:

rejectIndel 0
rejectREFValidREF 0
rejectREFValidALT 0
rejectLOWCOV_REF 0
rejectMap20 0
rejectLOWMQ 0
rejectLOWQUAL 0
rejectCloseIndels 0
rejectSysERR 0
rejectRM 0
rejectREF_unknownGeno 0
rejectedEMPTY 0
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'm not sure the command ended normally because there is a 'terminated' in it .

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It seems that the command ran ok, no sites were filtered out it seems.

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Thank you for you reply,but when I run the same code in shell srcipt ,it report an error,here is my script:

#!/bin/bash

#$ -cwd
#$ -j y
#$ -S /bin/bash

#$ -l mem_free=4G

export PATH=/ds3512/home/panyp/denovo/gcc-8.3/bin:$PATH
export PATH=/ds3512/home/panyp/denovo/gcc-8.3/lib64:$PATH
export LD_LIBRARY_PATH=/ds3512/home/panyp/denovo/gcc-8.3/lib64/:$LD_LIBRARY_PATH

export PATH=/ds3512/home/panyp/ruanjian/xz/bin:$PATH
export LD_LIBRARY_PATH=/ds3512/home/panyp/ruanjian/xz/lib:$LD_LIBRARY_PATH
export LDFLAGS="-L/ds3512/home/panyp/ruanjian/xz/lib"
export CFLAGS="-I/ds3512/home/panyp/ruanjian/xz/include"

VCFTOOLS=/share/apps/vcftools/vcftools-0.1.15
GLACTOOLS=/ds3512/home/panyp/750cexu/balance_selection/glactools-master
SAMTOOLS=/ds3512/home/panyp/ruanjian/samtools-1.9/bin
PYTHON=/ds3512/home/panyp/ruanjian/python36/bin/python

DIR=/ds3512/home/panyp/diff_genome/

$SAMTOOLS/samtools faidx Chr01.fa

$VCFTOOLS --vcf chr01.recode.vcf --indv Z-001 --out Z-001 --recode

$PYTHON vcf_modify.py Z-001.recode.vcf > final-Z-001.recode.vcf
$GLACTOOLS/glactools vcf2acf --fai Chr01.fa.fai --onlyGT final-Z-001.recode.vcf Z-001 > b.acf.gz
$GLACTOOLS/glactools view -h b.acf.gz|tail

here is my error:

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
Error: GlacParser tried to read 4 bytes but got 0

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Let's try viewing the file, can you run:

/ds3512/home/panyp/750cexu/balance_selection/glactools-master/glactools view a.acf.gz | head

and post the output?

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ok, thank you,grenaud.
there are two files "a.acf.gz" and "b.acf.gz" . the a.acf.gz is the result I got in command line and b.acf.gz is the result I got in shell script. here is their state . because the b.acf.gz is empty , I can't upload it.

[panyp@NCSI balance_selection]$ ll a.acf.gz b.acf.gz
-rw-rw-r-- 1 panyp panyp 541420 Jul 27 09:39 a.acf.gz
-rw-rw-r-- 1 panyp panyp 0 Jul 27 22:07 b.acf.gz

a.acf.gz

here is the result I run the "view" command:

[panyp@NCSI balance_selection]$ /ds3512/home/panyp/750cexu/balance_selection/glactools-master/glactools view a.acf.gz | head
Chr01 4485 G,A 0,0:0 0,0:0 0,2:0
Chr01 5564 C,N 0,0:0 0,0:0 2,0:0
Chr01 5698 C,N 0,0:0 0,0:0 2,0:0
Chr01 5899 T,C 0,0:0 0,0:0 0,2:0
Chr01 6035 G,A 0,0:0 0,0:0 0,2:0
Chr01 6324 C,N 0,0:0 0,0:0 2,0:0
Chr01 6333 C,N 0,0:0 0,0:0 2,0:0
Chr01 6443 A,G 0,0:0 0,0:0 0,2:0
Chr01 6474 C,N 0,0:0 0,0:0 2,0:0
Chr01 6483 G,N 0,0:0 0,0:0 2,0:0

[panyp@NCSI balance_selection]$ /ds3512/home/panyp/750cexu/balance_selection/glactools-master/glactools view b.acf.gz | head
Error: GlacParser tried to read 4 bytes but got 0.

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So it seems that the program works. I do not know what happens with the script, there could be an environment issue. I would need to login to diagnose. However, as nothing is wrong with the program, I would like to close the issue if that is ok with you?

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ok,thank you for your help. I will Contact my server administrator.

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