NGS pipeline error messages

[emeadd]

Hello. I ran the NGS pipeline for CYP2D6 and got a few error messages. When you have a chance, can you please let me know what they mean and if I need to re-run the analysis? The output files were still generated.

Message after alleles.zip file was created:
DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False. return cls(pd.read_table(fn))

Message after copy number.zip file was created:
Trying to unpickle estimator SVC from version 0.24.2 when using version 1.2.1. This might lead to breaking code or invalid results. Use at your own risk.
Trying to unpickle estimator LabelBinarizer from version 0.24.2 when using version 1.2.1. This might lead to breaking code or invalid results. Use at your own risk.
Trying to unpickle estimator OneVsRestClassifier from version 0.24.2 when using version 1.2.1. This might lead to breaking code or invalid results. Use at your own risk.

Thanks so much!

[sbslee]

@emeadd,

Please note that those messages are warnings, not errors. You can ignore them. See #57 for details.

P.S. In the future, could you please copy and paste the whole output? Example:

$ pypgx run-ngs-pipeline CYP2D6 grch37-CYP2D6-pipeline --variants "/home/ec2-user/PYPX/getrm-wgs-tutorial/grch37-variants.vcf.gz                                                                                                                             " --depth-of-coverage "/home/ec2-user/PYPX/getrm-wgs-tutorial/grch37-depth-of-coverage.zip" --control-statistics "/home/ec2-user/PYPX/getrm-wgs-tutorial/grch37-control-                                                                                                                             statistics-VDR.zip"
Saved VcfFrame[Imported] to: grch37-CYP2D6-pipeline/imported-variants.zip
Saved VcfFrame[Phased] to: grch37-CYP2D6-pipeline/phased-variants.zip
Saved VcfFrame[Consolidated] to: grch37-CYP2D6-pipeline/consolidated-variants.zip
Saved SampleTable[Alleles] to: grch37-CYP2D6-pipeline/alleles.zip
Saved CovFrame[ReadDepth] to: grch37-CYP2D6-pipeline/read-depth.zip
Saved CovFrame[CopyNumber] to: grch37-CYP2D6-pipeline/copy-number.zip
_/home/ec2-user/anaconda3/lib/python3.8/site-packages/sklearn/base.py:310: UserWarning: Trying to unpickle estimator SVC from version 0.24.2 when using version 0.24.1. T                                                                                                                             his might lead to breaking code or invalid results. Use at your own risk.
  warnings.warn(
/home/ec2-user/anaconda3/lib/python3.8/site-packages/sklearn/base.py:310: UserWarning: Trying to unpickle estimator LabelBinarizer from version 0.24.2 when using versio                                                                                                                             n 0.24.1. This might lead to breaking code or invalid results. Use at your own risk.
  warnings.warn(
/home/ec2-user/anaconda3/lib/python3.8/site-packages/sklearn/base.py:310: UserWarning: Trying to unpickle estimator OneVsRestClassifier from version 0.24.2 when using v                                                                                                                             ersion 0.24.1. This might lead to breaking code or invalid results. Use at your own risk.
  warnings.warn(_
Saved SampleTable[CNVCalls] to: grch37-CYP2D6-pipeline/cnv-calls.zip
Saved SampleTable[Genotypes] to: grch37-CYP2D6-pipeline/genotypes.zip
Saved SampleTable[Phenotypes] to: grch37-CYP2D6-pipeline/phenotypes.zip
Saved SampleTable[Results] to: grch37-CYP2D6-pipeline/results.zip

Also, I'd appreciate if you can first search for similiar Issues/Discussions within this repository before posting a new Issue :)