All studies in crdc/gdc Failed to validate

[jmtang2018]

Hi,

We are trying to import 43 studies in the "crdc/gdc" folder into our private installation of cbioportal. We got the same error in the validation for every study:

ERROR: meta_mrna_seq_fpkm.txt: Invalid stable id for genetic_alteration_type 'MRNA_EXPRESSION', data_type 'CONTINUOUS'; expected one of [mrna_U133, rna_seq_mrna, rna_seq_v2_mrna, rna_seq_v2_mrna_median_normals, mirna, mrna, rna_seq_mrna_capture, mrna_seq_cpm, mrna_seq_tpm, mrna_seq_fpkm_capture, mrna_seq_fpkm_polya]; value encountered: 'mrna_seq_fpkm'

ERROR: meta_mrna_seq_read_counts_zscores_ref_all_samples.txt: Invalid stable id for genetic_alteration_type 'MRNA_EXPRESSION', data_type 'Z-SCORE'; expected one of [mrna_U133_Zscores, rna_seq_mrna_median_Zscores, mrna_median_Zscores, rna_seq_v2_mrna_median_Zscores, rna_seq_v2_mrna_median_normals_Zscores, mirna_median_Zscores, mrna_merged_median_Zscores, mrna_zbynorm, mrna_seq_tpm_Zscores, mrna_seq_cpm_Zscores, rna_seq_mrna_capture_Zscores, mrna_seq_fpkm_capture_Zscores, mrna_seq_fpkm_polya_Zscores, mrna_U133_all_sample_Zscores, mrna_all_sample_Zscores, rna_seq_mrna_median_all_sample_Zscores, mrna_median_all_sample_Zscores, rna_seq_v2_mrna_median_all_sample_Zscores, rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores, mrna_seq_cpm_all_sample_Zscores, mrna_seq_tpm_all_sample_Zscores, rna_seq_mrna_capture_all_sample_Zscores, mrna_seq_fpkm_capture_all_sample_Zscores, mrna_seq_fpkm_polya_all_sample_Zscores, mrna_seq_fpkm_Zscores, mrna_seq_fpkm_all_sample_Zscores]; value encountered: 'mrna_seq_read_counts_Zscores'

Thanks,
Jeff

[rmadupuri]

Hi @jmtang2018, we will address this in the master branch. In the meantime, you can follow the solution provided in this discussion: https://groups.google.com/g/cbioportal/c/o7-H0RKueJc/m/9pgWCQLbAwAJ.