using custom glf instead of angsd output

[LZeitler]

Hi Filipe

When extracting GL tags from a vcf (called with freebayes) and converting to glf I am encountering some problems. NgsF does not want to process, I am wondering why. I know, it's not described in the readme and it's sort of file hacking but I don't see why it would be wrong. Maybe you can help.

Here my workflow

bcftools query -f '[%GL,]\n' my.vcf > my.gl
sed -i 's/\.,/0,0,0,/g' my.gl        # replace missing GL with 0,0,0,
sed -i 's/,/\t/g' my.gl                 # make tab sep
cat my.gl | perl -an -e 'for($i=1; $i<=$#F; $i++){print(pack("d",$F[$i]))}' > my.glf
N_IND=$(awk '{print NF/3; exit}' my.gl)
N_SITES=$(cat my.gl | wc -l)
cat my.glf | $NGSF --n_ind $N_IND --n_sites $N_SITES  --glf - --min_epsilon 0.001 \
       --out my.approx_indF --n_threads 1 --verbose 2 --approx_EM --seed 12345 --init_values r

output

 ==> Input Arguments:
    glf file: -
    init_values: r
    calc_LRT: false
    freq_fixed: false
    out file: fb_run5_all_nn_bi_mj_sn_mm.gl.0s.t.glf.approx_indF
    n_ind: 339
    n_sites: 489999
    chunk_size: 100000
    approx_EM: true
    call_geno: false
    max_iters: 1500
    min_iters: 10
    min_epsilon: 0.0010000000
    n_threads: 1
    seed: 12345
    quick: false
    verbose: 2
    version: 1.2.0-STD (Feb 23 2021 @ 12:18:32)

 ==> Analysis will be run in 5 chunk(s)
 ==> Using native I/O library

 [main] ERROR: cannot read GLF file!

 [main] ERROR: cannot read GLF file!
    : No such file or directory

[fgvieira]

What is the size, in bytes, of the my.glf file?

[LZeitler]

3982711872 bytes

[fgvieira]

Without looking at the files it is difficult, but it seems your GLF file might not be complete. The GLF file should have a size in bytes of = n_ind * n_sites * 3 * 8 (3 GL, and 8 for the size of a double).

maybe,
cat my.gl | perl -an -e 'for($i=1; $i<=$#F; $i++){print(pack("d",$F[$i]))}' > my.glf
should be:
cat my.gl | perl -an -e 'for($i=0; $i<=$#F; $i++){print(pack("d",$F[$i]))}' > my.glf

[LZeitler]

That was it, thanks!