Help with glf file - corrupt?

[Erikacj]

Hi. After I run the association test (-asso), I'm trying to test the .glf.gz file using the below code:

angsd \ -nThreads 8 \ -glf S6_output.glf.gz \ -fai reference.fasta.fai \ -ref reference.fasta \ -nInd 48 \ -doMajorMinor 4 \ -doMaf 2 \ -doAsso 1 \ -ybin pheno.txt \ -out S6_asso_test

But I keep getting this error:

-> angsd version: 0.932 (htslib: 1.10.2) build(Jul 13 2023 14:46:37)
-> Reading fasta: /Users/crl/omics/reference/Montipora_capitata_HIv1.assembly.fasta
-> Printing at chr: Montipora_capitata_HIv1___Scaffold_1___length_48529999 pos:249951 chunknumber 5000 contains 50 sites

[glfReader.cpp:fetch():34] Error reading full chunk: bytesRead:1536 expected:3840 will exit

What does this mean and how do I check whether the .glf.gz file is corrupted?

[ANGSD]

Normally this error occurs if a wrong number of individuals has been supplied or the glf file is truncated. Could you also supply us with the commands of how the glf file was generated?

On 18 Jul 2023, at 05.58, Erikacj @.***> wrote:

Hi. After I run the association test (-asso), I'm trying to test the .glf.gz file using the below code:

angsd -nThreads 8 -glf S6_output.glf.gz -fai reference.fasta.fai -ref reference.fasta -nInd 48 -doMajorMinor 4 -doMaf 2 -doAsso 1 -ybin pheno.txt -out S6_asso_test

But I keep getting this error:

-> angsd version: 0.932 (htslib: 1.10.2) build(Jul 13 2023 14:46:37) -> Reading fasta: /Users/crl/omics/reference/Montipora_capitata_HIv1.assembly.fasta -> Printing at chr: Montipora_capitata_HIv1_Scaffold1length_48529999 pos:249951 chunknumber 5000 contains 50 sites [glfReader.cpp:fetch():34] Error reading full chunk: bytesRead:1536 expected:3840 will exit

What does this mean and how do I check whether the .glf.gz file is corrupted?

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[Erikacj]

Sure. This is what I ran to get the .glf.gz file:

angsd \ -bam bamlist_no_out_reps.txt \ -nThreads 8 \ -ref reference.fasta \ -domajorminor 4 \ -dobcf 1 \ -gl 2 \ -domaf 1 \ -docounts 1 \ -dopost 1 \ -dogeno 8 \ -doGlf 3 \ -SNP_pval 2e-6 \ -minInd 40 \ -minmapQ 30 \ -minQ 20 \ -geno_minDepth 3 \ --ignore-RG 0 \ -dodepth 1 \ -dumpCounts 1 \ -doIbs 1 \ -makeMatrix 1 \ -doCov 1 \ -yBin pheno.txt \ -doAsso 1 \ -out no_out_reps

On Tue, Jul 18, 2023 at 12:55 AM ANGSD @.***> wrote:

Normally this error occurs if a wrong number of individuals has been supplied or the glf file is truncated. Could you also supply us with the commands of how the glf file was generated?

On 18 Jul 2023, at 05.58, Erikacj @.***> wrote:

Hi. After I run the association test (-asso), I'm trying to test the .glf.gz file using the below code:

angsd -nThreads 8 -glf S6_output.glf.gz -fai reference.fasta.fai -ref reference.fasta -nInd 48 -doMajorMinor 4 -doMaf 2 -doAsso 1 -ybin pheno.txt -out S6_asso_test

But I keep getting this error:

-> angsd version: 0.932 (htslib: 1.10.2) build(Jul 13 2023 14:46:37) -> Reading fasta: /Users/crl/omics/reference/Montipora_capitata_HIv1.assembly.fasta -> Printing at chr: Montipora_capitata_HIv1_Scaffold1length_48529999 pos:249951 chunknumber 5000 contains 50 sites [glfReader.cpp:fetch():34] Error reading full chunk: bytesRead:1536 expected:3840 will exit

What does this mean and how do I check whether the .glf.gz file is corrupted?

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[Erikacj]

Figured it out. I needed to run -glf 1, not -glf 3.

[victoria-gpr]

Hi, these days I have had the same problem. With -glf do you mean -doGlf? thank you.

[Erikacj]

Yes, -doGlf is the correct way to run it.