pmglab
commented
2 years ago @fmurgia
The parameter "--eqtl-file" is used to specify an eQTL file instead of a gene expression profile file (gtex.v8.gene.mean.tsv.gz). You can find the eQTL files under this folder.
Best,
PMGLab
Hi,
I'm trying using KGGSEE pipeline but I found some errors during reading gtex.v8.transcript.mean.tsv.gz file.
I'm reporting here the error:
@----------------------------------------------------------@ Effective settings: --nt 10 \ --sum-file test_4_pcga.txt.gz \ --chrom-col CHR \ --pos-col POS \ --p-col pvalue \ --gene-finemapping \ --eqtl-file ../Tools/kggsse/kggsee/resources/gtex.v8.gene.mean.tsv.gz \ --filter-eqtl-p 0.01 \ --vcf-ref ../Reference_data/1KG_p3_v5/VCF/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \ --out geneAssoceQTL \ --db-gene refgene,gencode \ --only-hgnc-gene \ --p-value-cutoff 0.05 \ --multiple-testing bonf \ --regions-out chr6:27477797-34448354 \ --expression-file ../Tools/kggsse/kggsee/resources/gtex.v8.transcript.mean.tsv.gz java.lang.NumberFormatException: For input string: "Name" at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054) at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110) at java.base/java.lang.Double.parseDouble(Double.java:543) at org.cobi.kggsee.controller.PValueReader.readeQTLPValuesFastAFormat(Unknown Source) at org.cobi.kggsee.CUIApp.parseeQTLPValueFile(Unknown Source) at org.cobi.kggsee.CUIApp.process(Unknown Source) at org.cobi.kggsee.CUIApp.main(Unknown Source) java.lang.Exception: java.lang.NumberFormatException: For input string: "Name" when parsing at line 2: Name Adipose-Subcutaneous.mean Adipose-Subcutaneous.SE Adipose-VisceralOmentum.mean Adipose-VisceralOmentum.SE AdrenalGland.mean AdrenalGland.SE Artery-Aorta.mean Artery-Aorta.SE Artery-Coronary.mean Artery-Coronary.SE Artery-Tibial.mean Artery-Tibial.SE Bladder.mean Bladder.SE Brain-Amygdala.mean Brain-Amygdala.SE Brain-AnteriorcingulatecortexBA24.mean Brain-AnteriorcingulatecortexBA24.SE Brain-Caudatebasalganglia.mean Brain-Caudatebasalganglia.SE Brain-CerebellarHemisphere.mean Brain-CerebellarHemisphere.SE Brain-Cerebellum.mean Brain-Cerebellum.SE Brain-Cortex.mean Brain-Cortex.SE Brain-FrontalCortexBA9.mean Brain-FrontalCortexBA9.SE Brain-Hippocampus.mean Brain-Hippocampus.SE Brain-Hypothalamus.mean Brain-Hypothalamus.SE Brain-Nucleusaccumbensbasalganglia.mean Brain-Nucleusaccumbensbasalganglia.SE Brain-Putamenbasalganglia.mean Brain-Putamenbasalganglia.SE Brain-Spinalcordcervicalc-1.mean Brain-Spinalcordcervicalc-1.SEBrain-Substantianigra.mean Brain-Substantianigra.SE Breast-MammaryTissue.mean Breast-MammaryTissue.SE Cells-Culturedfibroblasts.mean Cells-Culturedfibroblasts.SE Cells-EBV-transformedlymphocytes.mean Cells-EBV-transformedlymphocytes.SE Cervix-Ectocervix.mean Cervix-Ectocervix.SE Cervix-Endocervix.mean Cervix-Endocervix.SE Colon-Sigmoid.mean Colon-Sigmoid.SE Colon-Transverse.mean Colon-Transverse.SE Esophagus-GastroesophagealJunction.mean Esophagus-GastroesophagealJunction.SE Esophagus-Mucosa.mean Esophagus-Mucosa.SE Esophagus-Muscularis.mean Esophagus-Muscularis.SE FallopianTube.mean FallopianTube.SE Heart-AtrialAppendage.mean Heart-AtrialAppendage.SE Heart-LeftVentricle.mean Heart-LeftVentricle.SE Kidney-Cortex.mean Kidney-Cortex.SE Kidney-Medulla.mean Kidney-Medulla.SE Liver.mean Liver.SE Lung.mean Lung.SE MinorSalivaryGland.mean MinorSalivaryGland.SE Muscle-Skeletal.mean Muscle-Skeletal.SE Nerve-Tibial.mean Nerve-Tibial.SE Ovary.mean Ovary.SE Prostate.mean Prostate.SE Skin-NotSunExposedSuprapubic.mean Skin-NotSunExposedSuprapubic.SE Skin-SunExposedLowerleg.mean Skin-SunExposedLowerleg.SE SmallIntestine-TerminalIleum.mean SmallIntestine-TerminalIleum.SE Spleen.mean Spleen.SE Testis.mean Testis.SE Thyroid.mean Thyroid.SE Uterus.mean Uterus.SE Vagina.mean Vagina.SE at org.cobi.kggsee.controller.PValueReader.readeQTLPValuesFastAFormat(Unknown Source) at org.cobi.kggsee.CUIApp.parseeQTLPValueFile(Unknown Source) at org.cobi.kggsee.CUIApp.process(Unknown Source) at org.cobi.kggsee.CUIApp.main(Unknown Source)
I get same error using different Java version.
Any idea to solve the trouble?
Best,
Federico