A weired Site block all the progress?

[zhangshouwei309194]

Dear author:
Yesterday i goon trying. I extract just the first 20 sites to run "rvnp collapse", as a result it has been finished rapidly. Then i start to run gradiently. Finally i found a site, if it exists, it will stop the entire progress (rvnpl collapse). When i check the site, i cannot understood why it let rvnpl be still. Next i will describe the whole process of my exploring.

My pedfile:
family9 Q78 Q104 Q105 2 2
family9 Q79 Q104 Q105 2 2
family9 Q101 0 0 1 1
family9 Q103 Q104 Q105 2 2
family9 Q104 Q101 Q120 1 1
family9 Q105 0 0 2 1
family9 Q108 Q101 Q120 2 1
family9 Q109 Q101 Q120 2 2
family9 Q120 0 0 2 1
family10 Q114 0 0 2 1
family10 Q115 0 0 1 1
family10 Q116 Q115 Q114 2 1
family10 Q117 Q115 Q114 2 2
jinrong Q208A 0 0 1 1
jinrong Q209A 0 0 2 2
jinrong Q210A Q208A Q209A 2 1
jinrong Q212A Q208A Q209A 2 2
jinrong Q213A Q208A Q209A 2 1
jinrong Q214A Q208A Q209A 2 2
jinrong Q305 Q208A Q209A 1 1
jinrong Q306 Q305 Q308 2 2
jinrong Q307 Q305 Q308 1 1
jinrong Q308 0 0 2 1
jinrong q211B Q208A Q209A 2 2
weijun LN10 Q204A LN19 2 1
weijun LN11 LN20 Q202A 2 2
weijun LN19 0 0 2 1
weijun LN20 0 0 1 1
weijun Q202A Q204A LN19 2 2
weijun Q204A 0 0 1 1

command: rvnpl collapse --fam class2.final.m0to1.ped --vcf test.vcf.gz --output /path/rep1 --freq gnomAD_EAS -c 0.01 --rvhaplo

I tried the first 20 site, the first 40 sites,the first 60 sites and the first 80 sites. When my vcf include just the first 20 SNP, it has been finished, but 40, 60, 80 could not be finshed. The details are as follows. Then it never end from yesterday to now.
MESSAGE: Binary trait detected in [/annogene/cloud/bioinfo/PROJECT/RD/Pipeline_test/Public/shouweizhang/Analysis/B_MED-001/rvnpl_association/test/test_gradient/40/class2.final.m0to1.ped]
MESSAGE: Checking local resources 5/5 ...
MESSAGE: 30 samples found in [/annogene/cloud/bioinfo/PROJECT/RD/Pipeline_test/Public/shouweizhang/Analysis/B_MED-001/rvnpl_association/test/test_gradient/40/test_40.vcf.gz]
MESSAGE: 4 families with a total of 30 samples will be scanned for 28,488 pre-defined units
MESSAGE: 2 units processed {99.92%} ...

Later, i tried the first 30 snp site, it remains the same like this. Then i tried the first 28 , it keep the situation. Then i tried the first 26, it has been finished surprisingly. Then i tried the first 27, it could not be finished and remain the same like the situation except the first 20 and 26. So i guess it should be the SNP site to block the "rvnpl collapse". Later i remove this site and extract other first 40 site, it has been finised. i think the progress shoule be blocked by this site. The details of this site is as follows:
##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Q101 Q103 Q104 Q105 Q108 Q109 Q114 Q115 Q116 Q117 Q120 Q78 Q79 Q208A Q209A Q210A q211B Q212A Q213A Q214A Q305 Q306 Q307 Q308 LN10 LN11 LN19 LN20 Q202A Q204A
1 135982 rs368140013 A G 125.30 PASS gnomAD_EAS=1 GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 0|0
About this site, we just see two genotype 0|0 and 1|1, no 0|1, then i checked the first 26, it also have this situation. It‘s allele frequncy in "gnomAD_EAS" is 1, it will be filterd. But i don't know why it could block the "rvnpl collapse". Then i check my pedigree and the site's genotype, i could not get any rules.
Look foward to your reply! Thank you for your help.
Phillip

[gaow]

Finally i found a site, if it exists, it will stop the entire progress (rvnpl collapse).

Thanks for the forensics work -- this is very helpful! Could you send me the first 27 lines of your data? I cannot promise to fix it immediately as my schedule is quite full these days, but i'll try to find some time for it.

[zhangshouwei309194]

Thank you for your help. You can view the attachment.

rvnpl_relevant.zip