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SimurgArray/docs/messages.md
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kemal 0c5dd03ca8 PGx DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035) 
- scripts/pgx/fetch_sources.sh: CPIC API tables (CC0) into a dated folder with version and hashes.
- simurg/pgx/db.py: CPIC HGVS locations and values -> left-normalised VCF variants (SNV, del, ins, dup,
  repeats, delins, chrM); IUPAC values are core-allele wildcards; alleles without definitions are flagged.
- pipeline/pgx_db.py: deterministic SQLite (content-hash name), probe_map via the SNV VCF site mapper;
  GSA v4 PGx: 22 genes, 1354 alleles, 5002 probe links; two builds byte-identical.
2026-09-29 13:24:54 +01:00

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SimurgArray message catalogue

Generated from src/simurg/core/errors.py — do not edit by hand.

Code Level Meaning Spec
E_AUX_INVALID error Auxiliary-loci record is invalid OUT-035
E_BPM_CSV_MISMATCH error BPM and CSV manifests describe different loci IN-042
E_BPM_FORMAT error BPM manifest is malformed or unsupported IN-040
E_BUILD_MISMATCH error Manifest genome build differs from the FASTA build IN-063
E_CN_FAILED error CN calling failed for the sample CYTO-040
E_CN_SEX_UNRESOLVED error Sample sex unresolved and --unknown-sex-policy error CYTO-024
E_CN_SIDECAR_MISSING error cn_call_manifest.json not found in the cn call output CYTO-032
E_CN_VCF_UNINDEXED error CNV VCFs must be bgzipped and indexed for annotate CYTO-032
E_CONFIG_KEY error Unknown key in --config YAML CLI-019
E_CONFIG_PARSE error --config file is not valid YAML CLI-019
E_CSV_MANIFEST_FORMAT error CSV manifest is malformed IN-041
E_DUP_GTC error Several GTC files resolve to the same sample IN-030
E_DUP_IDAT error Several IDAT pairs resolve to the same sample IN-022
E_EGT_LOAD error Cluster (EGT) file cannot be loaded IN-044
E_EGT_MANIFEST_MISMATCH error Cluster file lacks loci of the manifest IN-043
E_FAI_MISMATCH error FASTA index does not match the FASTA IN-060
E_FASTA_FORMAT error FASTA file is malformed IN-060
E_FILE_NOT_FOUND error Input file or folder does not exist CLI-016
E_FILE_UNREADABLE error Input file cannot be read CLI-016
E_GTC_CORRUPT warning GTC file failed validation; sample skipped IN-032
E_GTC_UNSUITABLE error GTC lacks fields required by this command IN-031
E_IDAT_ENCRYPTED error Encrypted (version 1) IDATs are not supported IN-023
E_IDAT_FORMAT error IDAT file is malformed IN-023
E_IDAT_MANIFEST_MISMATCH error IDATs and manifest belong to different products IN-027
E_IDAT_PAIR_MISMATCH error Red and Grn IDATs of a sample do not match IN-023
E_INTERNAL error Internal error (bug); rerun with --debug and report CLI-014
E_METH_CONTROLS_FORMAT error Controls not formatted correctly. Must have 4 columns (Address,Type,Color_Channel,Name) MET-002
E_METH_MISSING_COLUMNS error Missing required columns in the methylation manifest MET-002
E_METH_NO_ASSAY error Probe section not found MET-002
E_METH_NO_CONTROLS error Missing control probes in manifest MET-002
E_METH_NO_IDATS error No IDATs found MET-004
E_METH_PREP_FAILED error Prep failed (sample) MET-010
E_MODEL_CLUSTER_MISMATCH error Input GTCs were called with another cluster file than the model IN-050
E_MODEL_MANIFEST_MISMATCH error Model was built for a different manifest probe set IN-051
E_MODEL_VERSION error Model schema is too old; rebuild it IN-051
E_NO_INPUT error Neither an input folder nor a sample sheet was given CLI-006
E_NO_INPUT_FOLDER error Sample sheet has no RootFolder and no folder was given CLI-006
E_OUTPUT_EXISTS error Outputs already exist; use --force or --resume CLI-010
E_PGX_BATCH_TOO_SMALL error Too few (passing) samples in the batch for PGx CN calling PCN-004
E_PGX_CN_FAILED error PGx CN calling failed for the sample PCN-002
E_PGX_SOURCE error PGx source tables missing; run scripts/pgx/fetch_sources.sh PGX-001
E_PGX_TRAIN_TOO_SMALL error Too few (passing) samples to train a PGx CN model PCN-005
E_QC_CONFIG_EXT error QC config file must be .yaml or .yml QC-021
E_QC_CONFIG_MISSING error QC config file does not exist QC-021
E_QC_CONFIG_PARSE error QC config file is not valid YAML QC-021
E_QC_CONFIG_STRUCTURE error QC config lacks the qc/report (QC/Report) wrapper QC-021
E_QC_DATASET_INCOMPLETE error Dataset folder lacks a required file QC-041
E_QC_FORMAT error Invalid --output-format value QC-063
E_QC_LABEL_COUNT error Number of labels does not match number of datasets QC-042
E_QC_LABEL_DUPLICATE error Dataset labels are not unique QC-042
E_QC_MIXED_TYPES error Genotyping and methylation datasets cannot be mixed QC-043
E_QC_NO_DATASETS error No QC dataset folder found QC-041
E_QC_PROFILE error Unknown QC profile QC-024
E_QC_THRESHOLD_KEY error Unknown QC threshold key QC-021
E_QC_THRESHOLD_RANGE error QC threshold value out of range QC-021
E_QC_THRESHOLD_VALUE error QC threshold value is not numeric or null QC-021
E_SHEET_BARCODE_FORMAT error Invalid SentrixBarcode_A / SentrixPosition_A value IN-007
E_SHEET_DELIMITER error Sample sheet is not comma-delimited CSV IN-001
E_SHEET_DUP_COLUMN error Duplicate column (column names are case-insensitive) IN-003
E_SHEET_DUP_SAMPLE error The same barcode/position appears in several rows IN-009
E_SHEET_EMPTY error Sample sheet has no data rows IN-001
E_SHEET_NAME_COLLISION error Sample names are not unique or clash with sample IDs IN-010
E_SHEET_NAME_EMPTY error Sample_Name is empty in at least one row IN-010
E_SHEET_NO_KEY_COLUMNS error Sample sheet lacks SentrixBarcode_A/SentrixPosition_A IN-002
E_SHEET_RESERVED error Sample sheet column collides with an output column IN-005
E_SHEET_TOO_LONG error Sample sheet name or value longer than 500 characters IN-006
I_CN_SEX_RESOLVED info Sample sex updated from U by the caller CYTO-024
I_UNLISTED_IDATS info IDAT pairs not listed in the sample sheet are ignored IN-016
W_CN_NO_FASTA warning No FASTA: VCF REF padding bases written as N CYTO-029
W_CN_PROBE_FLOOR warning Minimum probe count below 10 raised to 10 CYTO-008
W_CN_THRESHOLD_EXCEEDS_GENOME warning Size threshold exceeds the effective genome; no events CYTO-009
W_CTRL_DEFS_DIFFER warning BPM and CSV control definitions differ; the BPM wins QC-001
W_CTRL_MISSING warning Controls needed by a metric are absent; metric not evaluable QC-007
W_CTRL_ZERO_DIVISOR warning Control metric has a zero denominator (NaN) QC-008
W_DUP_IDAT_RESOLVED warning Duplicate IDAT pair resolved by --on-duplicate-idat IN-022
W_EGT_NAME warning Cluster file name is not portable IN-045
W_GTC_FOREIGN warning GTC was produced by another tool IN-031
W_IDAT_LOW_ADDRESS_COVERAGE warning Some manifest addresses are absent from the IDAT IN-027
W_IDAT_MANIFEST_NAME warning IDAT names a different manifest than the BPM IN-027
W_IDAT_NAME_MISMATCH warning IDAT barcode/position disagrees with its file name IN-023
W_IDAT_NO_SCAN_TIME warning IDAT has no scan entry in its run info IN-024
W_IDAT_UNPAIRED warning IDAT channel file without its partner IN-021
W_INDEL_PARTIAL_MATCH warning Indel source sequence matches the genome only partially OUT-019
W_INF1_NC_CONFLICT warning Infinium I no-call conflicts with other assays OUT-037
W_LARGE_OUTPUT warning Output will be very large EDGE-036
W_MANIFEST_NO_REFSTRAND warning Manifest lacks RefStrand annotation IN-040
W_MERGE_ALL_NC warning Every probe at a merged site is a no-call OUT-031
W_MERGE_AMBIGUOUS warning Probes at a site allow several genotypes; set missing OUT-031
W_MERGE_INCONSISTENT warning Probes at a site disagree; genotype set missing OUT-031
W_METH_MISSING_CONTROL_NAMES warning Control names missing from the manifest; metric set to NA MET-009
W_METH_MISSING_CONTROL_TYPES warning Control types missing from the manifest; metric set to NA MET-009
W_METH_MISSING_SAMPLE warning Missing sample: IDATs absent; the sample fails, the run continues MET-015
W_METH_NO_FEATURES warning No features, skipping PCA plot MET-013
W_MODEL_CLUSTER_MISMATCH warning Input GTCs were called with another cluster file than the model IN-050
W_NO_BGZIP warning Uncompressed VCF written; downstream commands need bgzip + index OUT-010
W_PGX_BATCH_BELOW_RECOMMENDED warning Fewer passing samples than recommended PCN-004
W_PGX_BATCH_COMPOSITION warning Batch spans several lots/batches or > 14 days of scans PCN-006
W_PGX_NO_ALT_CONTIG warning FASTA lacks a contig carrying a PGx region; REF written as N IN-062
W_PGX_REGION_FEW_PROBES warning PGx CN region has fewer than 10 unmasked probes PCN-008
W_QC_LABEL_SANITIZED warning Dataset label was sanitized QC-042
W_QC_NO_BAF warning GTC has no B-allele frequencies; contamination not estimated QC-064
W_QC_PEDIGREE warning Parent1/Parent2/Replicate value does not name a sample in the set IN-018
W_QC_TOO_FEW warning Too few samples or sites for a cohort QC statistic QC-026
W_QC_UNMATCHED_SAMPLES warning Sample IDs present in one QC file but not the other QC-040
W_REF_NOT_QUERIED warning The reference allele is not among the probe's alleles OUT-015
W_SHEET_BARCODE_REPAIRED warning Barcode written as a decimal was repaired IN-007
W_SHEET_EMPTY_COLUMN warning Columns with empty headers are ignored IN-004
W_SHEET_ROOTFOLDER_OVERRIDDEN warning CLI folder overrides the sheet RootFolder IN-008
W_SHEET_SEX_CONFLICT warning Reported-sex columns disagree IN-014
W_SKIP_AMBIGUOUS warning Ambiguous-strand locus dropped by --drop-ambiguous OUT-042
W_SKIP_CONTIG warning Manifest chromosome absent from the FASTA OUT-019
W_SKIP_EXCLUDED warning Locus excluded by --exclude-loci/--include-loci OUT-019
W_SKIP_INDEL_CONTEXT warning Indel sequence cannot be determined (no CSV SourceSeq) OUT-019
W_SKIP_INDEL_REF warning Indel reference allele cannot be determined from the FASTA OUT-019
W_SKIP_INTENSITY_ONLY warning Intensity-only locus was skipped OUT-019
W_SKIP_NO_STRAND warning Locus has neither RefStrand nor a sequence to align OUT-042
W_SKIP_UNMAPPED warning Locus without a genomic position was skipped OUT-019
W_UNKNOWN_LOCI warning Names in a locus list are not in the manifest OUT-036
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