hicPCA error

[MurliNair]

Hi, Thanks for developing HicExplorer and making it available to all. I am using hicInfo 3.7.2 and Python 3.10.6 I am following your protocol to analyze my HiCdata. Aligned using BWA and then created the matrix. Reviewed the plot before correcting the matrix. Plot is attached. I used the following to correct the matrix hicCorrectMatrix correct -m CON.h5 --filterThreshold -1 4 -o CON_correctedMinu1And4.h5

I want to make sure that the threshold I have used is correct.

When I run hicPCA hicPCA -m ../../hicBuildMatrix/CON/hiCmat1/CON_correctedMinu1And4.h5 \ --method lieberman \ --outputFileName CON_Minu1And4_pca1.bedgraph CON_Minu1And4_pca2.bedgraph CON_Minu1And4_pca3.bedgraph \ --format bedgraph

I get the following error Traceback (most recent call last): File "/work/mnair/anaconda3/envs/hiC/bin/hicPCA", line 7, in main() File "/work/mnair/anaconda3/envs/hiC/lib/python3.10/site-packages/hicexplorer/hicPCA.py", line 318, in main eigenvectors_correlate = np.hstack((eigenvectors_correlate, eigs[:, int(id) - 1:int(id)])) ValueError: invalid literal for int() with base 10: ' '

I have tried this several times and even changed the method and I keep getting the same error.

Thanks and look forward to your comments.

Cheers../Murli

[GiorgiaGiacomini]

I have the same issue. Did you solve it?

[MurliNair]

No I have not solved it yet. If I find a solution I shall post it here.

[DavidWarrenKatz]

Can someone please link to where the actual code for hicPCA is? I am having trouble finding it. Also, the Pearson matrix will have many NaNs. What is done about those before eigenvalues are computed?

[LHXqwq]

hicPCA -m BBL-1.h5 --outputFileName BBL-1-pca1.bw BBL-1-pca2.bw --format bigwig --whichEigenvectors 1 2 This line of code can run smoothly.

[thomasmanke]

Indeed. The number of --outputFileName has to match the number specified in --whichEigenvectors (or -we).