neoloop-caller IndexError

[zzhoujialu]

Dear author,
I conducted the same analytical strategy on a series of data from one dataset but come across the following error in one of them. I have no idea why it happens.

IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

My command line: neoloop-caller -O new.neo-loops.txt --assembly new.assemblies.txt --balance-type CNV --protocol insitu --prob 0.95 --nproc 4 -H /path/to/my/mcool/file::resolutions/50000 /path/to/my/mcool/file::resolutions/10000 /path/to/my/mcool/file::resolutions/5000

And here is part of my new.assemblies.txt file.

I used cooler dump to check those cool files and found no difference in file format. Could you give me any suggestions?
Looking forward to hearing from you. Really appreciate your help!
Yours sincerely,
kalo.

[XiaoTaoWang]

Hi Kalo, thanks for the feedback. Can you provide the full error message, so that I can debug?

[zzhoujialu]

Thanks! Here is my error message:

ARGUMENT LIST:
Output Path = new.neo-loops.txt
Cache Folder = .cache
SV assembly = new.assemblies.txt
Cooler List = ['/path/to/my/mcool/file::resolutions/50000 /path/to/my/mcool/file::resolutions/10000 /path/to/my/mcool/file::resolutions/5000']
Extended Genomic Span = 3000000bp
Balance Type = CNV
Probability threshold = 0.95
No pooling = False
Minimum marginal peaks = 2
Number of Processes = 4
Log file name = neoloop.log

[XiaoTaoWang]

Basically this error might be caused when the reconstructed matrix for an SV is either too sparse or too small in size. I just fixed this bug in the version 0.4.3-r1, can you upgrade your package by running pip install -U neoloop and try again?

[zzhoujialu]

Hi, Thank you for your prompt reply！

I successfully installed neoloop-0.4.3 but I still get the same error...
I checked my new.assemblies.txt file and found 61 rows.
And here is my cool file information (at the resolutions of 50000):

"bin-size": 50000,
"bin-type": "fixed",
"creation-date": "2023-02-12T08:52:31.400557",
"format": "HDF5::Cooler",
"format-url": "https://github.com/4dn-dcic/hic2cool",
"format-version": 3,
"generated-by": "hic2cool-0.8.3",
"genome-assembly": "/path/to/hg38.chrom.sizes",
"hicFileScalingFactor": 1.0,
"nbins": 62130,
"nchroms": 195,
"nnz": 124458497,
"nviIndex": "0000000000000000",
"nviLength": "0000000000000000",
"software": "Juicer Tools Version 1.11.09",
"storage-mode": "symmetric-upper"

Can I assume that my reconstructed matrix is not sparse or small or is there something wrong with my understanding...
Could you give me any suggestions? Thanks! :)

[XiaoTaoWang]

double check to make sure your neoloop version is 0.4.3-r1, but not 0.4.3?

[zzhoujialu]

Great! That works.