molgenis / systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
https://github.com/molgenis/systemsgenetics/wiki
GNU General Public License v3.0
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difficults in using Genotype Harmonizer #637

Open malu-rdz opened 1 year ago

malu-rdz commented 1 year ago

Hi, I'm just trying to use Genotype Harmonizer and it was not working. So, I tried to just run the examples, exactly as the files were downloaded but, it is not working too. The message below was shown to me. Any ideia what I'm doing wrong? Thank you

: not foundnaryPlinkExample.sh: 2: : not foundnaryPlinkExample.sh: 4: HarmonizeBinaryPlinkExample.sh: 5: cd: can't cd to . : not foundnaryPlinkExample.sh: 6: : not foundmonizer.sh: 2: : not foundmonizer.sh: 4: : not foundmonizer.sh: 6: /GenotypeHarmonizer.jar jarfile . HarmonizeBinaryPlinkExample.sh: 8: --inputType: not found HarmonizeBinaryPlinkExample.sh: 9: --input: not found HarmonizeBinaryPlinkExample.sh: 10: --update-id: not found HarmonizeBinaryPlinkExample.sh: 11: --outputType: not found HarmonizeBinaryPlinkExample.sh: 12: --output: not found HarmonizeBinaryPlinkExample.sh: 13: --refType: not found HarmonizeBinaryPlinkExample.sh: 14: --ref: not found : not foundnaryPlinkExample.sh: 15: : not foundnaryPlinkExample.sh: 16:

/exampleOutput/ed in: .

malu-rdz commented 1 year ago

When trying it with my files, it appears the following message:

: not foundHarmonizer.sh: 2: : not foundHarmonizer.sh: 4: : not foundHarmonizer.sh: 6: /GenotypeHarmonizer.jar jarfile ..