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Atkinson-Lab / Tractor

Scripts for implementing the Tractor pipeline
MIT License
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Error in ExtractTracks.py Script #6

Closed EEPuckett closed 3 years ago

EEPuckett commented 3 years ago

I have encounted the following error a few times using the updated ExtractTracts script: Traceback (most recent call last): File "/home/puckett3/software/Tractor/ExtractTracts.py", line 163, in <module> extract_tracts(**vars(args)) File "/home/puckett3/software/Tractor/ExtractTracts.py", line 106, in extract_tracts geno_b = str(geno[1]) IndexError: list index out of range

I have checked that the number of samples in the VCF is half the number in the MSP file. I have also run the script changing the second header line in the MSP file from:

chm spos epos sgpos egpos n snps

to

chm spos epos sgpos egpos nsnps

Yet I get the same error.

Do you have any suggestions for troubleshooting?

With thanks, Emily

eatkinson commented 3 years ago

resolved over email. VCF file was for the entire genome, msp were split by chromosome, causing alignment issues. Earlier versions of this script (https://github.com/eatkinson/Tractor/blob/06275533632103ab5b6520f1365f2692a3039923/ExtractTracts.py) are less flexible for ancestry numbers but do not require files to be harmonized in this way. To be updated: allow for chrom msp input in updated script