Kim Rutherford

Unstable output for owltools --save-closure-for-chado

8

This is a follow on from https://github.com/pombase/pombase-chado/issues/678 We're using `owltools --save-closure-for-chado` to generate the closure we load into Chado. @ValWood noticed that the output changes regularly for parts of the...

Parse error using .obo URLs

18

Hi. We're seeing a problem with .obo URLs using the 2020-04-06 release. Command lines this work fine: ``` owltools http://purl.obolibrary.org/obo/cl.owl --ancestors neuron ``` But changing to a `.obo` purl results...

ClassCastException / crash when running --make-species-subset

7

Hi. We're having trouble with processing the latest go-plus.owl with owltools. With this command line: (cd /tmp/; wget http://purl.obolibrary.org/obo/go/extensions/go-plus.owl) && (cd go-svn/ontology/extensions; owltools /tmp/go-plus.owl --use-catalog --reasoner elk --make-species-subset -t NCBITaxon:4896...

Terms are not completely removed by --make-species-subset

7

I'd like to get an OBO file of GO terms that make sense for pombe. I've tried: ``` owltools go-plus.obo --reasoner elk --make-species-subset -t NCBITaxon:4896 -o -f obo go-pombe-subset.obo ```...

"Assertion `numStrings < MAX_ELEMS' failed"

6

While running sga index I get this: ``` Building index for preprocessed.fastq in memory using ropebwt done bwt construction, generating .sai file sga: SampledSuffixArray.cpp:163: void SampledSuffixArray::buildLexicoIndex(const BWT*, int): Assertion `numStrings...