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cytham / nanovar

Structural variant caller for low-depth long-read sequencing data
GNU General Public License v3.0
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IndexError : list index out of range #71

Closed skeremaydin closed 10 months ago

skeremaydin commented 11 months ago

nanovar -t 24 /truba/home/saaydin/nanopore_wgs/bamfiles/minimap/DRR258593.bam /truba/home/saaydin/nanopore_wgs/reference_genomes/Homo_sapiens_assembly38.fasta /truba/home/saaydin/nanopore_wgs/nanovar/vcf_files/DRR258593/ I run this code but took this bug WhatsApp Image 2023-12-19 at 20 07 22

cytham commented 11 months ago

Hi @skeremaydin, what is your NanoVar version? Can you please try with the latest version on GitHub?

git clone https://github.com/cytham/nanovar.git 
cd nanovar 
pip install .

Can you also please make sure your reference genome chromosome names does not contain [ ~ : - ] characters?

skeremaydin commented 11 months ago

Thank you for replying. I checked my reference genome, it does not contain those symbols. If you install with pip, you can have version 1.5.0. Yet, when you install the package with mamba or conda from the bioconda, the 1.2.7 version is installed. When 1.5.0 version one is run, ModuleNotFoundError: No module named 'cytocad' error occurs, whereas in 1.2.7 version, the IndexError : list index out of range error persist.

cytham commented 11 months ago

Hi @skeremaydin, thanks for letting me know the bioconda issue, it might be due to dependency clashes. Did you install NanoVar on a freshly created conda environment?

Please install it through GitHub for now, the Pip version has a bug. Here's how to do it:

git clone https://github.com/cytham/nanovar.git 
cd nanovar 
pip install .
skeremaydin commented 11 months ago

Hello again. Yes, I did. I could install the 1.5.0 version of nanovar in a new created environment. Yet, this time I get this error AttributeError: module 'numpy' has no attribute 'object'. np.object was a deprecated alias for the builtin object. To avoid this error in existing code, use object by itself. Doing this will not modify any behavior and is safe. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations Thank you for your help. I am gonna try what I can do and find solution.

cytham commented 11 months ago

Did you try installing from github?

skeremaydin commented 11 months ago

Your instructions helped me solve my problem. Thank you very much!