Question: AssertionError: error loading tabix index for vcf.gz file
0
gravatar for alaa.khan.16
13 days ago by
alaa.khan.160 wrote:

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?

software error • 82 views
ADD COMMENTlink modified 12 days ago • written 13 days ago by alaa.khan.160

yes I tried this and i got a message tbx_index_build failed

ADD REPLYlink written 12 days ago by alaa.khan.160

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

ADD REPLYlink written 12 days ago by Pierre Lindenbaum133k

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

ADD REPLYlink written 12 days ago by ATpoint44k

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

ADD REPLYlink written 12 days ago by alaa.khan.160
0
gravatar for Pierre Lindenbaum
13 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

did you index your vcf.gz with tabix ?

tabix -p vcf data/ceph1463.peddy.vcf.gz
ADD COMMENTlink written 13 days ago by Pierre Lindenbaum133k
0
gravatar for alaa.khan.16
12 days ago by
alaa.khan.160 wrote:

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

ADD COMMENTlink written 12 days ago by alaa.khan.160
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