Counting issue: failed to map segment from shared object

CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

MIT License

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Counting issue: failed to map segment from shared object #524

Closed CWYuan08 closed 1 year ago

CWYuan08 commented 2 years ago

Hi,

I was trying to run umi_tools count --per-gene --gene-tag=XT -I assigned_sorted.bam -S counts.tsv.gz for my file, but I keep getting the ImportError: miniconda3/envs/squire/lib/python2.7/site-packages/scipy/optimize/_cobyla.so: failed to map segment from shared object

Could you please help me on this?

Thank you!

Best regards, CW

TomSmithCGAT commented 2 years ago

Hi. It looks like you're using python 2.7. Unfortunately, we no longer support python 2. Could you try updating to python 3 please.

CWYuan08 commented 2 years ago

Thank you I updated to python 3, but for any umitools command, I keep getting :" Segmentation fault"

Do you know why this is?

Thank you very much!

TomSmithCGAT commented 2 years ago

Have you re-installed umi_tools? Are you using a package manager, e.g conda/mamba?