x object 'GWAS_CITATION' not found

brucemoran commented 4 years ago

Hi Sigve,

I'm getting the below error.

Can you give an idea?

Singularity container is library://bruce.moran/default/projects:somatic_n-of-1.centos7.conda.

Command:

cpsr.py  \  
  --no-docker  \
  --no_vcf_validate \
  --panel_id 0 \
  --query_vcf test.hc.merge.vcf.gz \
  --pcgr_dir pcgr \
  --output_dir ./ \
  --genome_assembly grch38 \
  --conf pcgr/data/grch38/cpsr_configuration_default.toml \
  --sample_id test

Error: Problem with `filter()` input `..1`.
x object 'GWAS_CITATION' not found
i Input `..1` is `!is.na(GWAS_HIT) & !is.na(GWAS_CITATION)`.
Backtrace:
    x
 1. +-pcgrr::generate_cpsr_report(...)
 2. | +-dplyr::filter(calls, !is.na(GWAS_HIT) & !is.na(GWAS_CITATION))
 3. | \-dplyr:::filter.data.frame(calls, !is.na(GWAS_HIT) & !is.na(GWAS_CITATION))
 4. |   \-dplyr:::filter_rows(.data, ...)
 5. |     +-base::withCallingHandlers(...)
 6. |     \-mask$eval_all_filter(dots, env_filter)
 7. \-base::.handleSimpleError(...)
 8.   \-dplyr:::h(simpleError(msg, call))

sigven commented 4 years ago

Thanks for reporting. I'll have a look.

sigven commented 4 years ago

Hi Bruce,

Figured it out. Try making your Singularity version with the dev version of PCGR (docker pull sigven/pcgr:dev), and clone the updated cpsr.py script from the repo. I believe your test run should work now.

thanks, Sigve

brucemoran commented 4 years ago

Thanks Sigve,

I'm just going to roll back to previous versions as I make one big container for my workflow from conda, so would need to set up a lot of things to make it work, when previous does the job!

Appreciate the quick responses as ever,

Bruce

On Mon, 5 Oct 2020 at 00:04, Sigve Nakken notifications@github.com wrote:

Hi Bruce,

Figured it out. Try making your Singularity version with the dev version of PCGR (docker pull sigven/pcgr:dev), and clone the updated cpsr.py script from the repo. I believe your test run should work now.

thanks, Sigve

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sigven/cpsr/issues/30#issuecomment-703328729, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABY27MT5GSJH4Z6BXPD4VM3SJD5QZANCNFSM4SD5QNMA .

sigven / cpsr

x object 'GWAS_CITATION' not found #30