freezing after starting script

[EtieM]

Hello,

I have the following error when running shllowHRD script:

/Rscript Tools/shallowHRD/shallowHRD_hg19_1.13_controlfreec_chrX.R /shallow/Results/23D2655750/FREEC/23D2655750_chr.bam_ratio.txt /shallow/Results/23D2655750/shallowHRD/ Tools/shallowHRD/cytoband_adapted_hg19.csv

======================================================== Sample : 23D2655750_chr ========================================================

Fast gathering segments 1... Message d'avis : NAs introduits lors de la conversion automatique Find Threshold 1... Erreur dans seqlevels[rankSeqlevels(seqlevels)] <- seqlevels : NAs interdits dans les affectations indicées Appels : makeGRangesFromDataFrame Erreur dans h(simpleError(msg, call)) : erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction 'subsetByOverlaps' : objet 'GRanges_object_ratio_file' introuvable Appels : subsetByOverlaps -> .handleSimpleError -> h

Can you help me?

Thanks

[aeeckhou]

Hello,

I can try at least!

Did you generate your file with controlFREEC ? If so provide me your config file. Also can you provide me your ratio file?

Best, Alexandre

[EtieM]

Yes it was generated with ControlFREEC. Here are the files: config_WGS.txt 23D2655750_chr.bam_ratio.txt

Thanks!

[aeeckhou]

Hello,

I think I found the problem ! You have aligned to reference genome with contigs (Un_gl000247, Un_gl000233....), not just 1->22 + X + Y.

In the Prerequisities you have this:

"IMPORTANT: Please only use chromosomes 1 to 22 (plus the Chromosome Y if you want to) for the alignment step. Additionnal chromosomes (contigs) might introduce errors."

I am mostly sure the freeze comes at the very least from this!

Try realigning your fastqs (or at least delete the contigs in your controlFREEC ratio file) and then rerun the algorithm.

Kepp me posted, Alexandre Eeckhoutte

[EtieM]

Thanks, it works!