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mancusolab / ma-focus

MA-FOCUS: Multi-Ancestry Fine-mapping Of CaUsal gene Sets
GNU General Public License v3.0
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Error: reset_index() got an unexpected keyword argument 'names' #22

Closed maegsul closed 10 months ago

maegsul commented 10 months ago

Hi,

First of all, thank you for developing this tool, I have been using FOCUS for a long time now and it has been very useful for me, so thanks!

I have recently switched to MA-FOCUS (v0.803) as FOCUS is deprecated, however I receive the error "reset_index() got an unexpected keyword argument 'names'":

[2023-11-15 01:28:25 - INFO] Find 22 common genes to be fine-mapped at region 11:46370397-11:48370397. [2023-11-15 01:28:25 - INFO] Running TWAS. [2023-11-15 01:28:25 - ERROR] reset_index() got an unexpected keyword argument 'names' [2023-11-15 01:28:25 - INFO] Finished TWAS & fine-mapping. Thanks for using FOCUS, and have a nice day!

I am testing MA-FOCUS with this example code:

focus finemap gwas_input.tsv.gz ldref.chr11 eqtldatabase.db --out test --chr 11 --p-threshold 1E-5 --plot --verbose --locations regionsToTest.bed

Of note, here gwas_input.tsv.gz file has a tab-delimited header "CHR SNP BP A1 A2 Z N" and --locations file is with tab-delimited header: "chrom start stop".

Can you please help me with this error? Thanks in advance!

Best, Fahri

maegsul commented 10 months ago

The problem was solved after updating python from 3.6 to 3.9, and upgrading pandas to 2.1.3 and numpy to 1.23.1.