kemal
1cb7b59559
noise-outlier exclusion + robustness test (PCN-017/EDGE-026), platform from the CSV manifest (CLI-032) Also: star-allele calls are checked for one manifest/build per run (PGX-011), duplications at the CN cap are named xN (PGX-022), and tandem names attach supporting variants to their full copy.
131 lines
11 KiB
Markdown
131 lines
11 KiB
Markdown
# 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_CN_MISSING` | error | A sample has no PGx CN VCF (give --no-cn to run without) | PGX-011 |
|
|
| `E_PGX_GUIDELINE` | error | Guideline tables not present in the PGx DB | PGX-025 |
|
|
| `E_PGX_PLATFORM_UNKNOWN` | error | PGx CN platform (LCG/EX) unknown: give --csv or --platform | CLI-032 |
|
|
| `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_PGX_VCF_UNINDEXED` | error | SNV VCFs for PGx must be bgzipped and indexed | PGX-011 |
|
|
| `E_PGX_VCF_UNSUITABLE` | error | SNV VCF unsuitable for PGx (squashing/locus filters/foreign) | PGX-011 |
|
|
| `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_NO_PROBE_MAP` | warning | The PGx DB has no probe map for this manifest | PGX-035 |
|
|
| `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 |
|