Problem reading full chunk error

[AdamStuckert]

Hi,

I am using ngsRelate version 2, and getting an error that hasn't already been raised in issues. I followed the template on the GitHub page. My code:

angsd -b samples4relatedness.txt -out angsd4relatedness -gl 2 -domajorminor 1 -snp_pval 1e-6 -domaf 1 -minmaf 0.05 -doGlf 3 -P 15

zcat angsd4relatedness.mafs.gz | cut -f5 | sed 1d > freq.txt

ngsRelate -g angsd4relatedness.glf.gz -n 100 -p 15 -f freq.txt -O output.res

I get the following error:

        -> Frequency file: 'freq.txt' contain 1458673 number of sites
        -> Problem reading full chunk

Thanks in advance,
Adam

[ANGSD]

Could you supply me with the number of lines ith tne freqfile, and the uncompressed filesize of angsd4relatedness.glf.gz. wc -l freq.txt gunzip -c angsd4relatedness.glf.gz |wc -c Best Den man. 13. maj 2019 kl. 14.33 skrev Adam Stuckert < notifications@github.com>:

…

Hi, I am using ngsRelate version 2, and getting an error that hasn't already been raised in issues. I followed the template on the GitHub page. My code: angsd -b samples4relatedness.txt -out angsd4relatedness -gl 2 -domajorminor 1 -snp_pval 1e-6 -domaf 1 -minmaf 0.05 -doGlf 3 -P 15 zcat angsd4relatedness.mafs.gz | cut -f5 | sed 1d > freq.txt ngsRelate -g angsd4relatedness.glf.gz -n 100 -p 15 -f freq.txt -O output.res I get the following error: -> Frequency file: 'freq.txt' contain 1458673 number of sites -> Problem reading full chunk Thanks in advance, Adam — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#20?email_source=notifications&email_token=ABQOR3W3NZRMBEFPWJFK6Y3PVFNYFA5CNFSM4HMPLCDKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GTNKZFQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABQOR3RMG2IOAC6O5KPT6KTPVFNYFANCNFSM4HMPLCDA> .

[AdamStuckert]

Number of lines in the frequency file: 1458673

angsd4relatedness.glf.gz size: 1575366840

Thanks,
Adam

[ANGSD]

So by the filesize alone the glf file looks corrupted. Do you have 100 individuals as suggested by the -n 100 argument for ngsRelate?