Hi, I have come across this error while running pixy. Do you know how to fix it? Thanks for your help!
Here is the log:
pixy --stats dxy --vcf pixy_input_10chrom.vcf.gz --window_size 10000 --populations pop.txt --chromosomes 'Scaffold_6;HRSCAF=40'
[pixy] pixy 1.2.7.beta1
[pixy] See documentation at https://pixy.readthedocs.io/en/latest/
/home/edgar/miniconda3/envs/pixy/lib/python3.8/site-packages/allel/io/vcf_read.py:1732: UserWarning: invalid INFO header:
[pixy] Validating VCF and input parameters...
[pixy] Checking write access...OK
[pixy] Checking CPU configuration...OK
[pixy] Checking for invariant sites...OK
[pixy] Checking chromosome data...OK
[pixy] Checking intervals/sites...OK
[pixy] Checking sample data...OK
[pixy] All initial checks past!
[pixy] Preparing for calculation of summary statistics: dxy
[pixy] Data set contains 2 population(s), 1 chromosome(s), and 12 sample(s)
[pixy] Window size: 10000 bp
[pixy] Started calculations at 14:45:32 on 2023-02-28
[pixy] Using 1 out of 32 available CPU cores
[pixy] Processing chromosome/contig Scaffold_6;HRSCAF=40...
IndexError: list index out of range
Hi, I have come across this error while running pixy. Do you know how to fix it? Thanks for your help!
Here is the log:
pixy --stats dxy --vcf pixy_input_10chrom.vcf.gz --window_size 10000 --populations pop.txt --chromosomes 'Scaffold_6;HRSCAF=40' [pixy] pixy 1.2.7.beta1 [pixy] See documentation at https://pixy.readthedocs.io/en/latest/ /home/edgar/miniconda3/envs/pixy/lib/python3.8/site-packages/allel/io/vcf_read.py:1732: UserWarning: invalid INFO header:
[pixy] Validating VCF and input parameters... [pixy] Checking write access...OK [pixy] Checking CPU configuration...OK [pixy] Checking for invariant sites...OK [pixy] Checking chromosome data...OK [pixy] Checking intervals/sites...OK [pixy] Checking sample data...OK [pixy] All initial checks past!
[pixy] Preparing for calculation of summary statistics: dxy [pixy] Data set contains 2 population(s), 1 chromosome(s), and 12 sample(s) [pixy] Window size: 10000 bp
[pixy] Started calculations at 14:45:32 on 2023-02-28 [pixy] Using 1 out of 32 available CPU cores
[pixy] Processing chromosome/contig Scaffold_6;HRSCAF=40... IndexError: list index out of range