Unknown Error

[nicholas-moskwa]

Hi @yycunc
I have been working with your FIREcaller analysis and for a subset of my samples and when I run the FIREcaller() function I get this error:

Error in remove_mhc(y6, gb, res) : object 'y2' not found

Have you ever seen this before or know what it is referring too?

I am running FIREcaller on Human data that has been separated into individual chromosome matrices.

I don't think it has anything to do with the mappability file, because as far as I can tell the mappability file has the right format. Please share if you have any ideas. Thanks.

[nicholas-moskwa]

Never mind. Figured it out.

[nicholas-moskwa]

Actually related to your 'gb' input, I am working with human data, built using GRCh38, but I cannot use 'GRCh38' as an input for 'gb', it gives this error:

Error : It seems your species name is wrong or UCSC does not provide cytoband
data for your species or internet connection was interrupted. If
possible, download cytoBand file from
https://hgdownload.cse.ucsc.edu/goldenPath/GRCh38/database/cytoBand.txt.gz
and use read.cytoband(file).

Error : It seems your species name is wrong or UCSC does not provide chromInfo
data for your species or internet connection was interrupted. If
possible, download chromInfo file from
https://hgdownload.cse.ucsc.edu/goldenPath/GRCh38/database/chromInfo.txt.gz
and use read.chromInfo(file).

Error: Cannot download either cytoband or chromInfo file from UCSC.

[yycunc]

Actually related to your 'gb' input, I am working with human data, built using GRCh38, but I cannot use 'GRCh38' as an input for 'gb', it gives this error:

Error : It seems your species name is wrong or UCSC does not provide cytoband data for your species or internet connection was interrupted. If possible, download cytoBand file from https://hgdownload.cse.ucsc.edu/goldenPath/GRCh38/database/cytoBand.txt.gz and use read.cytoband(file).

Error : It seems your species name is wrong or UCSC does not provide chromInfo data for your species or internet connection was interrupted. If possible, download chromInfo file from https://hgdownload.cse.ucsc.edu/goldenPath/GRCh38/database/chromInfo.txt.gz and use read.chromInfo(file).

Error: Cannot download either cytoband or chromInfo file from UCSC.

Hi nicholas,

I have revised the script to fix this error. Would you please re-install it and try again? I would this time it works on GRCh38.

Bests,

Yuchen