Open Accompany0313 opened 3 months ago
yezhengSTAT
commented
3 months ago Sorry for my late reply. It seems that "res" may not be calculated successfully. Maybe you can check the pickle output of res, which is saved by the command before the error was triggered?
if saveFlag: with open(outdir + '/pickle/res', 'wb') as f: pickle.dump(res, f)
Also, did the demo data work?
Thanks, Ye
Accompany0313
commented
2 months ago I try to save the intermediate results and generate the res file, but I can't seem to open the file.
The command I use is as follows： python scripts/scVI-3D.py -b 10 -c "whole" -r 1000000 -i "tan2021/data/raw" -o "tan2021/results" -cs "tan2021/tan2021-metadata.txt" -g "supplementaryData/mm10.chrom.sizes" -s -n 100 -gpu -p 1 -pca 50 -up -tp -v
Thanks！
Accompany0313
commented
2 months ago The res output from here is all 0.0, and the type is list, and the error is still AttributeError: 'NoneType' object has no attribute 'groupby'
The command I use is as follows： python scripts/scVI-3D.py -b 10 -pool 1 -c "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr1,chr20,chr21,chr22" -r 1000000 -i "Lee2019/GSE130711/raw" -o "Lee2019/results" -cs "Lee2019/GSE130711-metadata.txt" -g "supplementaryData/hg19.chrom.sizes" -s -br -n 100 -gpu -p 1 -pca 50 -up -tp -v
Hi Ye, Nice work!
When I tried to process the Lee et al. 2019. dataset, I got the following error: Traceback (most recent call last): File "scripts/scVI-3D.py", line 757, in
for cellId, cellDf in res[i][1].groupby('cellID'):
AttributeError: 'NoneType' object has no attribute 'groupby'
My cellsummary file format is as follows:
Could you please help me with it? Thank you so much!