Issue with glf file - too many sites

[dgallery]

Hi,
I am trying to make a kinship matrix from 47 individuals. I am running the following code:

angsd -b bams_qst_adults -gl 2 -domajorminor 1 -snp_pval 1e-6 -domaf 1 -minmaf 0.05 -doGlf 3 -out kinMAT
zcat kinMAT.mafs.gz | cut -f5 |sed 1d > freq
./ngsRelate -g kinMAT.glf.gz -n 47 -f freq -O kinMAT

Which produces the following error file:

./ngsRelate -g kinMAT.glf.gz -n 47 -f freq -O kinMAT
-> Seed is: 1211251308
-> Frequency file: 'freq' contain 139458 number of sites
-> Too many sites in glf file. Looks out of sync, or make sure you supplied correct number of individuals (-n)
-> Or that the number of sites provided (-L) it is correct

I double checked that my file list contains 47 individuals. Any assistance you can provide would be greatly appreciated.
Thanks!

[ANGSD]

Sorry for late reply. If this is still relevant. Please supply files.

Thanks!

[dgallery]

Here you go: The files are too large to fit so I've attached a link to them in Dropbox: https://www.dropbox.com/sh/sle2vmlvc8jr6sb/AAD4vYwjyYn7Mo6xxDrYDtwia?dl=0

This is my input code:
#make glf and mafs files
echo "/work/07707/dgallery/ls6/software/angsd/angsd -b bams_kinship -gl 2 -domajorminor 1 -snp_pval 1e-6 -domaf 1 -minmaf 0.05 -doGlf 3 -out kinMAT" > kins
ls6_launcher_creator.py -j kins -n kins -t 2:00:00 -e $email -w 1 -a $allo
sbatch kins.slurm

#remove header from mafs
zcat kinMAT.mafs.gz | cut -f5 |sed 1d >freq

#make kinship matrix
echo "/work/07707/dgallery/ls6/software/ngsRelate/ngsRelate -g kinMAT.glf.gz -n 65 -f freq -O kinMAT" > kins2
ls6_launcher_creator.py -j kins2 -n kins2 -t 2:00:00 -e $email -w 1 -a $allo
sbatch kins2.slurm

Thank you for your help!

[RRSingleton]

Hi, was this issue ever resolved? I'm running into the same problem. When I check my glf file, it has the the same number of site as my freq file (69671) and I have the right number of individuals in my glf file (152). Here's the code I used, and links to my files:

#for NGSrelate
nohup angsd -GL 1 -out genolike -nThreads 20 -doGlf 4 -doMajorMinor 1 -SNP_pval 1e-6 -doMaf 1 -bam all.list &

#NGSrelate
zcat genolike.mafs.gz | cut -f5 |sed 1d >freq
nohup ./../NGSrelate/ngsRelate/ngsRelate -g genolike.glf.gz -n 152 -L 69671 -O ngsRelate.out &

mafs: https://drive.google.com/file/d/1s9JM-n2tQ7Pih9zav-_4PQ1LOT95ZNn-/view?usp=sharing
glf: https://drive.google.com/file/d/1GjexTxYJMi3CV8yJk1SpOqC68534Xebn/view?usp=sharing
freq: https://drive.google.com/file/d/1vnoIeJVmfmI3kBdFcOZYfam3ps7yZ6Di/view?usp=sharing

Thank you!

[dgallery]

I never got it to work. Still get the error when I try to run my code.

[RRSingleton]

Did you find an alternate program to use? I've used READ, but want a second method to verify.

[ANGSD]

i dont understand the ngsrelate command you are not specifying the freqfile?

…

On 16 Nov 2023, at 22.15, RRSingleton ***@***.***> wrote: Did you find an alternate program to use? I've used READ, but want a second method to verify. — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQOR3QXQJXTNZKWQZY2AD3YEZ7A3AVCNFSM6AAAAAAU6OQ3CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJVGMZDMNJWGU>. You are receiving this because you commented.

[RRSingleton]

Whoops, sorry, that was me just changing flags around to see if i could get a different error. Here's what I used: ./../NGSrelate/ngsRelate/ngsRelate -g genolike.glf.gz -n 152 -f freq -O ngsRelate.out

[ANGSD]

Its been some time that I used the program myself, but I am sure it works. Can you try adding the number of sites when you are supplying the freq file.

…

-L 69671 If it doesnt work then please do wc all.list and wc freq and let me know what it prints.

On 16 Nov 2023, at 22.43, RRSingleton ***@***.***> wrote: Whoops, sorry, that was me just changing flags around to see if i could get a different error. Here's what I used: ./../NGSrelate/ngsRelate/ngsRelate -g genolike.glf.gz -n 152 -f freq -O ngsRelate.out — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABQOR3WLO5QL5YBDBOBE2GDYE2CHXAVCNFSM6AAAAAAU6OQ3CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJVGM3DAOJSGU>. You are receiving this because you commented.

[RRSingleton]

I've tried that, but it returns the same error.

[RRSingleton]

and here's the wc returns:

152 152 6212 all.list
69671 69671 627039 freq

[KHanghoj]

Hi all. Have you checked that angsd did not stop prematurely. You can either check the log or use the r script in the bottom of the readme.

…

On Sun, Nov 19, 2023 at 4:36 PM RRSingleton ***@***.***> wrote: and here's the wc returns: 152 152 6212 all.list 69671 69671 627039 freq — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD4IO6QJKSCIORGY4ARRO5TYFIRPXAVCNFSM6AAAAAAU6OQ3CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJXHA4TAMJVGY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[RRSingleton]

The end of the angsd run log has the runtime and everything looks good. I also re-ran angsd with an abridged sample set and get the same error.

[KHanghoj]

Have you loaded the data into r and ensured you can fill the matrix?

…

On Sun, Nov 19, 2023 at 9:41 PM RRSingleton ***@***.***> wrote: The end of the angsd run log has the runtime and everything looks good. I also re-ran angsd with an abridged sample set and get the same error. — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD4IO6XDJ6SWKT6DMOQQ4TLYFJVH3AVCNFSM6AAAAAAU6OQ3CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJXHE3TCNBTGU> . You are receiving this because you commented.Message ID: ***@***.***>

[RRSingleton]

It ran without errors, here's the output
outfile.zip

[ozgurtoprak08]

hello I am having the same problem have you figured it out?

[dgallery]

Yes, I used this version of angsd, which worked: angsd version: 0.939-4-gdc62e26 (htslib: 1.14-9-ge769401) build(Aug 9 2022 11:18:05)

…

On Tue, Apr 2, 2024 at 6:07 AM ozgurtoprak08 ***@***.***> wrote: hello I am having the same problem have you figured it out? — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASBQZGIZLQVQAN2WIIDSBFDY3KGORAVCNFSM6AAAAAAU6OQ3CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZRG4YTMOBTHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ozgurtoprak08]

Thank you very much, I also tried adding -sites 1KGsites.txt at the code and it seems to work Best regards, Toprak

…

On Tue, Apr 2, 2024, 17:25 dgallery ***@***.***> wrote: Yes, I used this version of angsd, which worked: angsd version: 0.939-4-gdc62e26 (htslib: 1.14-9-ge769401) build(Aug 9 2022 11:18:05) On Tue, Apr 2, 2024 at 6:07 AM ozgurtoprak08 ***@***.***> wrote: > hello I am having the same problem have you figured it out? > > — > Reply to this email directly, view it on GitHub > <#47 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ASBQZGIZLQVQAN2WIIDSBFDY3KGORAVCNFSM6AAAAAAU6OQ3CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZRG4YTMOBTHE> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BHQ3NUNDVBOUKCPTV3OMW43Y3LEV5AVCNFSM6AAAAAAU6OQ3CCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZSGM2TQMZQG4> . You are receiving this because you commented.Message ID: ***@***.***>