Gene_Centric_Coding output ERROR messages

[DamienTan]

Hi Dr. Li Sorry to bother you again. I met some ERROR messages when I ran Gene Centric Coding analysis. Here are the part of the log file.

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     used (Mb) gc trigger (Mb) max used (Mb)

Ncells 269062 14.4 654557 35 444157 23.8 Vcells 448534 3.5 8388608 64 1771722 13.6 [1] 379 [1] 51 # of selected samples: 772 # of selected variants: 280 # of selected samples: 772 # of selected variants: 6 # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 1 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : Number of rare variant in the set is less than 2! # of selected samples: 772 # of selected variants: 5 # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 3,197,953 [1] 52 # of selected samples: 772 # of selected variants: 24 # of selected samples: 772 # of selected variants: 6 # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 \ # of selected variants: 3 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : Number of rare variant in the set is less than 2! # of selected samples: 772 # of selected variants: 3 # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 3,197,953 [1] 53 # of selected samples: 772 # of selected variants: 163 # of selected samples: 772 # of selected variants: 10 # of selected samples: 772 # of selected variants: 1 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : Number of rare variant in the set is less than 2! # of selected samples: 772 # of selected variants: 1 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : Number of rare variant in the set is less than 2! # of selected samples: 772 # of selected variants: 5 # of selected samples: 772 # of selected variants: 4 # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 3,197,953 [1] 54 # of selected samples: 772 # of selected variants: 37 # of selected samples: 772 # of selected variants: 1 # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 1 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : Number of rare variant in the set is less than 2! # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 3,197,953 [1] 55 # of selected samples: 772 # of selected variants: 76 # of selected samples: 772 # of selected variants: 11 # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 4 # of selected samples: 772 # of selected variants: 7 # of selected samples: 772 # of selected variants: 0 Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff, : genotype is not a matrix! # of selected samples: 772 # of selected variants: 3,197,953

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I don't know if the Error messages will interrupt the next steps. Could you give some advice? Looking forward to yout reply. Damien

[xihaoli]

Hi Damien,

Thanks for letting me know. I can confirm that these messages are not errors from your scripts, but they serve as indications of certain functional categories of genes that do not have at least 2 rare variants to form a variant set. Please feel free to go ahead; this will not interrupt the next steps.

Best, Xihao

[DamienTan]

That is inspiring! Thanks so much for your reply.

[xihaoli]

You're very welcome, Damien!