AssertionError: error loading tabix index for vcf.gz file

Question

[alaa.khan.16]

Dear all

I am running peddy command python -m peddy -p 4 --plot --prefix ceph-1463 data/ceph1463.peddy.vcf.gz data/ceph1463.ped

however each time I got an error: AssertionError: error loading tabix index for data/ceph1463.peddy.vcf.gz I make sure that I am working on the same directory where these two vcf and ped files are placed

Any Idea how to solve this error please?

[alaa.khan.16]

yes I tried this and i got a message tbx_index_build failed

[Pierre Lindenbaum]

I'm sure that is not the only error message that was displayed....

[ATpoint]

Then please show all relevant code. If the indexing failed then either because the file is corrupted, not sorted, or not properly compressed.

[alaa.khan.16]

the first peddy command: python -m peddy -p 4 --plot --prefix Alaa_burden-2021 myFile.vcf.gz myFile.ped

and from this I got AssertionError: error loading tabix index for akhan_all_samples_peddy.vcf.gz

Then I used the command: tabix -p vcf myFile.vcf.gz and from this i got the error tbx_index_build failed: myFile.vcf.gz

I re compressed the vcf file using bgzip -c myFile.vcf > myFile.vcf.gz after that tabix -p vcf myFile.vcf.gz , but I am stillgetting same error of failure of tbx_index_build

That is all commands I used to be able to run peddy

Answer 1

[Pierre Lindenbaum]

did you index your vcf.gz with tabix ?

tabix -p vcf data/ceph1463.peddy.vcf.gz

Answer 2

[alaa.khan.16]

another error has appeared when i reperformed the indexing which is the present string not recognised. Not really sure how to solve this i am stick with this many days