Hello Hail team, I am running into an error when running count after filtering on either columns or rows. mt = get_gnomad_data('genomes', adj=True, release_annotations=True, split=True) mt = hl.filter_intervals(mt, hl.experimental.get_gene_intervals(gene_symbols=['AP4B1','AP4E1', 'AP4M1', 'AP4S1']…

Sorry…I cannot for the life of me figure out how to attach a file on here. Google has failed me. How should I send it?

This is prehaps non-intuitive or just aggressively intuitive, but you should be able to drag and drop? I just fixed the file extensions to permit .log files. foo.log (9 Bytes)

Yup now I can. Before it would only accept image extensions. Thank you. gnomad_clinvar.log (403.8 KB)

aha: (TableRead Table{global:Struct{},key:,row:Struct{s:String}} False “{"name":"TableNativeReader","path":"gs://gnomad/hardcalls/hail-0.2/mt/exomes/gnomad.exomes.mt/cols","_spec":{"name":"TableSpec","file_version":65536,"hail_version":"devel-a23032101373","references_rel_path":"…/references","tab…

I’m fairly confident I back-patched (read: manually edited the metadata.json.gz) all the gnomAD files, so unless there’s another issue, I would think it should work.

Maybe try a different file (the exomes, or non-split hardcalls) to double check, maybe I missed one, but this one’s a pretty big workhorse, so I’d be surprised. mt = mt.select_globals() can also work to check if that’s the issue.

I fixed the error message here to give us more information. Can you try running on latest master? (if you need help building from source, let me know)

mt = get_gnomad_data('exomes', adj=True, release_annotations=True, release_samples=True, split=True) mt = mt.select_globals() mt.count() Fails with the same error. I attempted to build from source but received this error when running ./install-gcs-connector.sh ERROR: (gcloud.iam.service-accounts…

This code works for me with my home-spun 9c44fc9e7c2b (or maybe 22f6defd17d who knows with my rig anymore, anyway relatively recent) so I don’t think it’s the old requiredness problem.

@mwilson I mean try on the cloud with a custom build – to do this you do (from hail/hail): HAILCTL_BUCKET_BASE="gs://a-bucket-you-can-write-to" make install-hailctl

Error when running count after filtering MT

Hail Query & hailctl

tpoterba October 8, 2019, 9:12pm 22

oops… this should fix… https://github.com/hail-is/hail/pull/7230

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Error when running count after filtering MT

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