raphael-group / STARCH

Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
MIT License
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AttributeError: 'STARCH' object has no attribute 'means' #4

Open hzongyao opened 3 years ago

hzongyao commented 3 years ago

I use this code python run_STARCH.py -i ./DATA --output DMG -t 10 -m hgTables_hg19.txt -c 3 The 10X directory containing barcodes.tsv, features.tsv, matrix.mtx, and tissue_positions_list.csv The outcome is as follow:

Traceback (most recent call last): File "run_STARCH.py", line 34, in operator = STARCH(i,n_clusters=n_clusters,num_states=3,normal_spots=normal_spots,beta_spots = beta_spot,nthreads=nthreads,gene_mapping_file_name=gene_m_mapping_file_name) File "/mnt/raid/tmp/workflow/STARCH/STARCH.py", line 141, in init logger.info('starting means: '+str(self.means)) AttributeError: 'STARCH' object has no attribute 'means'

WandeRum commented 3 years ago

I have the same issue.

lucaskerr commented 3 years ago

I also have the same issue; image attached. I tried some simple tweaks to both the run_Starch.py and Starch.py scripts but no luck on my end. Any advice?

Screen Shot 2021-09-25 at 9 56 41 PM
braphael8 commented 3 years ago

Can you tell us the machine type and Python version that you are using? We have seen this issue sporadically on some installations but not on others.

lucaskerr commented 3 years ago

Thanks for your reply! I'm on a 2019 Macbook Pro, Big Sur Version 11.6. Python version 3.8.8. Considering your comment, I just tried running the Starch scripts again on a 2018 PC running Windows 10, Python version 3.7, but I ran into the same error: 'STARCH' object has no attribute 'means'.

huoyuying commented 2 years ago

I have the same issue.

Can you solve this problem now? I have the same issue !

whitneyt1 commented 8 months ago

has anyone been able to solve this? When running this on 36 reactions with n_clusters= 1, 2, 3 it successfully runs on all reactions except one reaction repeatedly receives this error when n_clusters=1

thank you!