This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Incorrect gvcfServerPath for reference genome

Hello

I'm using the latest PHG and I'm on step 3: imputing haplotypes. I am having a problem with an incorrect gvcfServerPath I had put in my initial genomeData file. It has stopped me at the HaplotypeGraphBuilderPlugin.

[pool-1-thread-1] DEBUG net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin - genome path variable must be a semi-colon separated string, with the first portion indicating the server address, e.g. server;/path/to/file. Error on genomePath

Is there anyway to correct this path in the database, or do I have to rerun the entire pipeline from the beginning?

phg
• 1,219 views • link
written by wcs98 • wcs98

1 answer

Yes, you can correct it in the database. Enter your database and find the ids you'd like to change with a query something like:

select id, genome_path, genome_file from genome_file_data where type=2;

That query will show you the paths for the gvcf files (type "2" are entries for just the gvcf files)

You can then change the ids you want changed with the command:

update genome_file_data set genome_path='host;/my/gvcf/path' where id=20;

Example from a test db I have:

phgsmallseq=# select id,genome_path, genome_file from genome_file_data where type=2;
 id |               genome_path               |                   genome_file                    
----+-----------------------------------------+--------------------------------------------------
  2 | localhost;/Users/lcj34/temp/gvcfRemote/ | Ref_Assembly.gvcf.gz
  4 | localHost;/remoteGvcfs/                 | LineA.gvcf.gz
  6 | localHost;/remoteGvcfs/                 | LineB.gvcf.gz
  7 | localhost;/Users/lcj34/temp/gvcfRemote/ | Ref_haplotype_caller_output_filtered.g.vcf.gz
  8 | localhost;/Users/lcj34/temp/gvcfRemote/ | RefA1_haplotype_caller_output_filtered.g.vcf.gz
  9 | localhost;/Users/lcj34/temp/gvcfRemote/ | LineB1_haplotype_caller_output_filtered.g.vcf.gz
 10 | localhost;/Users/lcj34/temp/gvcfRemote/ | LineA_haplotype_caller_output_filtered.g.vcf.gz
 11 | localhost;/Users/lcj34/temp/gvcfRemote/ | LineB_haplotype_caller_output_filtered.g.vcf.gz
 12 | localhost;/Users/lcj34/temp/gvcfRemote/ | LineA1_haplotype_caller_output_filtered.g.vcf.gz
(9 rows)

phgsmallseq=#

phgsmallseq=# update genome_file_data set genome_path='132.236.88.4;/Users/lcj34/temp/gvcfRemote/' where id=2;
UPDATE 1
phgsmallseq=#

Then check by listing them again:

phgsmallseq=# select id,genome_path, genome_file from genome_file_data where type=2 order by id;
 id |                genome_path                 |                   genome_file                    
----+--------------------------------------------+--------------------------------------------------
  2 | 132.236.88.4;/Users/lcj34/temp/gvcfRemote/ | Ref_Assembly.gvcf.gz
  4 | localHost;/remoteGvcfs/                    | LineA.gvcf.gz
  6 | localHost;/remoteGvcfs/                    | LineB.gvcf.gz
  7 | localhost;/Users/lcj34/temp/gvcfRemote/    | Ref_haplotype_caller_output_filtered.g.vcf.gz
  8 | localhost;/Users/lcj34/temp/gvcfRemote/    | RefA1_haplotype_caller_output_filtered.g.vcf.gz
  9 | localhost;/Users/lcj34/temp/gvcfRemote/    | LineB1_haplotype_caller_output_filtered.g.vcf.gz
 10 | localhost;/Users/lcj34/temp/gvcfRemote/    | LineA_haplotype_caller_output_filtered.g.vcf.gz
 11 | localhost;/Users/lcj34/temp/gvcfRemote/    | LineB_haplotype_caller_output_filtered.g.vcf.gz
 12 | localhost;/Users/lcj34/temp/gvcfRemote/    | LineA1_haplotype_caller_output_filtered.g.vcf.gz
(9 rows)

phgsmallseq=#
• 0 views • link
updated by GenoMax GenoMax • written by lcj34 lcj34

Thank you very much, this worked perfectly. I was also able to fix incorrect paths I had for the other gvcfs.

• 0 views • link
written by wcs98 • wcs98

Log in to answer this question.

More posts like this