Closed drneavin closed 5 years ago
I'm getting the same error and would love some help as well! I tried the pip version and GitHub version, and also tried with and without providing it a vcf file, to no avail.
There was a bug and was fixed in the newest github release. Will update pip version later.
Thanks Jon, the new script for main.py that you updated works well.
In addition, I would like to match the samples across the batches using SNP genotype data. Would there be a way for me to have the code report the SNP genotypes for each cluster across more than just the distinguishing variants? In other words, could I have the script output a matrix of all the SNPs with the cluster SNP genotypes?
Good to hear @drneavin ! For the genotype question, please refer to new thread #4
@AmandaKedaigle sorry, did it solve your issue as well, please?
@AmandaKedaigle sorry, did it solve your issue as well, please?
Yes it did, it's working for me now as well. Thanks!
Great to know! @AmandaKedaigle
Hello!
I am trying to run scSplit to demultiplex samples on which I do not have SNP genotype data. I have successfully run matrices.py and received the alt and ref csvs. However, when I try to run main.py, I receive an error. Here is the complete output of the error:
Traceback (most recent call last): File "/home/drenea/venv/3.6/lib/python3.6/site-packages/scSplit/main.py", line 356, in
main()
File "/home/drenea/venv/3.6/lib/python3.6/site-packages/scSplit/main.py", line 334, in main
model.distinguishing_alleles(pos)
File "/home/drenea/venv/3.6/lib/python3.6/site-packages/scSplit/main.py", line 249, in distinguishing_alleles
proj[i, j] = np.matmul(U[:,i], subt.iloc[j])
ValueError: setting an array element with a sequence.
I have checked my csv files generated from matrices.py and they appear to be what I would expect. The command that I'm running is: python $scSplitDIR/main.py -r ref_filtered.csv -a alt_filtered.csv -n 5
I do receive an scSplit.log file which starts with these lines: Starting data collection: 2019-06-24 17:03:32.422419 Allele counts matrices uploaded: 2019-06-24 17:03:34.924011
And then in records ~10,000 iterations but no other files from the run are generated. I am running with the pip installed version of scSplit but also tried with the main.py from Github. I am running with R 3.6.5.
Any help would be much appreciated!
-Drew