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thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data
http://chibba.pgml.uga.edu/snphylo/
GNU General Public License v2.0
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Exluding all SNPs on non-autosomes #30

Open daneshnedaie opened 5 years ago

daneshnedaie commented 5 years ago

Hello I'm getting a problem of all my SNPs being excluded, can anyone give me a fix?

[1] 136020 [1] 136747 [1] 137458 [1] 138157 [1] 138886 [1] 139597 [1] 140278 [1] 140967 [1] 141694 [1] 142395 [1] 143102 [1] 143777 [1] 144507 [1] 145225 [1] 145915 [1] 146640 [1] 147342 [1] 148066 [1] 148841 [1] 149558 Tue Mar 12 12:05:13 2019 Done. Hint: it is suggested to call snpgdsOpen' to open a SNP GDS file instead ofopenfn.gds'. SNP pruning based on LD: Excluding 150,225 SNPs on non-autosomes Error in .InitFile2(cmd = paste(ifelse(inherits(gdsobj, "SeqVarGDSClass"), : There is no SNP! Calls: snpgdsLDpruning -> .InitFile2 -> .Call Execution halted

What can I do to fix this error?

AudryZhao commented 5 years ago

hi, I got the same error. have you fixed it yet? thanks.

nedoluzhko commented 5 years ago

Also, got the same error. Now, I am trying to change my code using this: https://github.com/thlee/SNPhylo/issues/27. Previously, I have launched SNPhylo through the command: snphylo.sh -A -b -r -v salmon.vcf.

nedoluzhko commented 5 years ago

Tried: snphylo.sh -v salmon.vcf -r -P test -B 1000

[1] 39545 Mon May 13 16:42:39 2019 Done. Hint: it is suggested to call snpgdsOpen' to open a SNP GDS file instead ofopenfn.gds'. SNP pruning based on LD: Excluding 39,872 SNPs on non-autosomes Error in .InitFile2(cmd = paste(ifelse(inherits(gdsobj, "SeqVarGDSClass"), : There is no SNP! Calls: snpgdsLDpruning -> .InitFile2 Execution halted

The same! Any ideas?

nedoluzhko commented 5 years ago

I have found a decision: https://www.biostars.org/p/83232/

You have to change chromosomes ID in our multiVCF, or in reference genome file to numbers. In my case, I have changed fasta ID to the numbers using this command: awk '/^>/{print ">" ++i; next}{print}' old.fa > new.fa, then I have created a new.vcf.

AudryZhao commented 5 years ago

Changing ID works for me! THANKS!!!

Hengfu-Yin commented 5 years ago

Thanks! @AudryZhao @nedoluzhko It worked for me when I changed the chromosome ID with numbers; also I noticed that the length of number mattered. It didn't work if the number was too long!

zuzmus commented 5 years ago

hey, for those facing the same problem (as the others might have solved it in the meantime). I was getting the same, there is a not so nice feature that by default, any number higher than 22 is consider a non-autosome: [-a The_number_of_the_last_autosome (22)].

Simply fix it by adding -a 10000 in the command (or whatever number, which is higher than your highest chr number:-)