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ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
115 stars 14 forks source link

Problem running pi on pixy #74

Closed bvaditi closed 1 year ago

bvaditi commented 1 year ago

I have created a vcf file with invariant site using bcftools and pixy installation seems to be fine. Yet on running the following code

pixy --stats pi --vcf filename.vcf.gz --populations Pops.txt --window_size 1 --output_folder Data/ --output_prefix pixytrial

Gives the error:

/home/uramakri/bvaditi/.conda/envs/pixy/lib/python3.8/site-packages/allel/io/vcf_read.py:1732: UserWarning: invalid INFO header: '##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n' warnings.warn('invalid INFO header: %r' % header)

[pixy] Validating VCF and input parameters... [pixy] Checking write access...OK [pixy] Checking CPU configuration...OK [pixy] Checking for invariant sites...OK tabix: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory [pixy] Checking chromosome data...subprocess.CalledProcessError: Command 'tabix -l /home/uramakri/bvaditi/filename.vcf.gz' returned non-zero exit status 127.

I am not able to figure what is causing the error. Could you please let me know?

ksamuk commented 1 year ago

Hi there! This looks to me like tabix may be installed incorrectly, or is conflicting with another piece of software in your environment (samtools often is the cause with libcrypto.so.1.0.0). What I'd try is to make a new conda environment for just pixy and tabix, and try running it again.

bvaditi commented 1 year ago

Dear Keiran, Thanks for your response. I am able to run now but there is still the warning for vcf header. The output file has a lot of NAs. I am attaching it here. Will it be possible to check whether it is ok? Thanks and advance. pixytrial_pi.txt

ksamuk commented 1 year ago

Hi there, pixy will output NAs if there is no data (variant or invariant) in the targeted window. The way to confirm that is correct is to look at your VCF and see if there are indeed no sites, or only sites with all missing genotypes, in the windows with all NAs.

kanikaghildiyal commented 1 year ago

Hello, While running the pixy software after converting vcf file with invariant sites using bcftools, I am getting the following error: UnicodeDecodeError:'utf-8' codec cant decode byte0x8b in position 1:invalid start byte

kanikaghildiyal commented 1 year ago

Could you please help me on this issue?