search

kkdey / GSSG

Gene Set + S2G strategy annotations analyzed for disease architecture
45 stars 12 forks source link

Please help with this erorrs #1

Closed bitcometz closed 2 years ago

bitcometz commented 2 years ago

Hi, I try to run the demo, but it reports the errors:

ERROR: Unable to locate a modulefile for 'gcc/6.2.0'
ERROR: Unable to locate a modulefile for 'R'

Best

kkdey commented 2 years ago

Hi @bitcometz , the module load ... lines are for user on a cluster. If you are running the script in a local machine with both gcc snd R on the path, you can just comment out these lines.

bitcometz commented 2 years ago

Thanks for your reply !!!

I try your method and it works. But I met another problem in the demo:

out1 = ABC_intergenic_bedgraph_calc(scores,
                                    output_cell = paste0(bed_dir, "/", annot_name),
                                    output_bed = paste0("ABC.bed")
                                   )

Eorros:

Error in names(x) <- value: 'names' attribute [4] must be the same length as the vector [0]
Traceback:

1. ABC_intergenic_bedgraph_calc(scores, output_cell = paste0(bed_dir, 
 .     "/", annot_name), output_bed = paste0("ABC.bed"))
2. `colnames<-`(`*tmp*`, value = c("chr", "start", "end", "TargetGene"))

Could you help with this problem?

Thanks !!!

bitcometz commented 2 years ago

Is something wrong with the *.gz files in the URL: https://alkesgroup.broadinstitute.org/LDSCORE/Dey_Enhancer_MasterReg/processed_data/

2021-06-28T18:18:19.153Z        0.1 kB         ABCpaper_NasserFulcoEngreitz2020_Blood_AvgHiC.txt.gz

The sizes of *.gz file are very small. Could you help with this problem?

And I cannot find the above file in another URL:

https://alkesgroup.broadinstitute.org/LDSCORE/DeepLearning/Dey_DeepBoost_Imperio/data_extra/

Thanks !!!