assembly missing, all variants ignored

[martiliasf]

• Do you want to request a feature or report a bug?

bug and features

• What is the current behavior?

assembly missing, all vcf entries skipped

pharmcat -vcf ../hg38_align_wes/admin_installed_pgkb-ngs/first_run.vcf.calls.vcf -o .
2019-12-11 14:57:00,455 INFO o.p.p.PharmCAT [PharmCAT.java:130] Using alleles: /org/pharmgkb/pharmcat/definition/alleles
2019-12-11 14:57:00,481 INFO o.p.p.PharmCAT [PharmCAT.java:131] Using annotations: /org/pharmgkb/pharmcat/reporter/guidelines
2019-12-11 14:57:00,482 INFO o.p.p.PharmCAT [PharmCAT.java:132] Writing to: .
2019-12-11 14:57:00,488 INFO o.p.p.PharmCAT [PharmCAT.java:149] Run time: Wed Dec 11 14:57:00 EST 2019
2019-12-11 14:57:00,595 WARN o.p.p.v.m.ContigMetadata [ContigMetadata.java:94] Required metadata property "assembly" is missing
--- lots of lines like this---
2019-12-11 14:57:00,792 WARN o.p.p.v.m.ContigMetadata [ContigMetadata.java:94] Required metadata property "assembly" is missing
2019-12-11 14:57:00,804 WARN o.p.p.v.VcfParser [VcfParser.java:94] There are 1 samples in the header but 0 in the metadata
2019-12-11 14:57:00,808 WARN o.p.p.h.VcfReader [VcfReader.java:141] Ignoring chr1:1

The input files are the vcf files from your ngs pipeline: https://github.com/PharmGKB/pgkb-ngs-pipeline . Firstly, i've tried multiple of the vcf files that the pipeline creates, none of them work. The above example uses the calls file. It would be great if some documentation clearly stated which vcf from the ngs pipeline should be used as input to the pharmcat.

• If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar.

• What is the expected behavior?

the expected behavior is to create the pharmcat output.... ??

• What is the motivation / use case for changing the behavior?

• Please tell us about your environment:

  • PharmCAT Version: ???
  • JDK Version: [ JDK8 | OpenJDK | etc ]
  • Environment: [ Windows | macOS | Linux distro | etc ]

pharmcat/0.7.0-27
[martyf@c0928 pharmcat]$ java -version
java version "10.0.2" 2018-07-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.2+13)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.2+13, mixed mode)

linux, i think its research linux, some variant of redhat.

You should indicate version in your --help output.

• Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, eg. stackoverflow, gitter, etc)

The software was installed by the server sysadmins.

[martiliasf]

issue resolved by fixing pgkb hg38 alignment pipeline here:
PharmGKB/pgkb-ngs-pipeline#5 (comment)