{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS7640LVLT/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7640LVLT",
"aliases": [
"igvf:s"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Reference file [IGVFFI3505JBSU](/reference-files/IGVFFI3505JBSU/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/reference-files/IGVFFI3505JBSU/"
},
{
"category": "upload status not validated",
"detail": "Reference file [IGVFFI7020OYZY](/reference-files/IGVFFI7020OYZY/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/reference-files/IGVFFI7020OYZY/"
},
{
"category": "inconsistent document type",
"detail": "Alignment file [IGVFFI4478TORF](/alignment-files/IGVFFI4478TORF/) has `file_format_specification` [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/) with `document_type` plasmid map. File format specifications are excepted to be documents have type file format specification.",
"level": 60,
"level_name": "ERROR",
"name": "audit_file_format_specifications",
"path": "/alignment-files/IGVFFI4478TORF/"
},
{
"category": "upload status not validated",
"detail": "Alignment file [IGVFFI4478TORF](/alignment-files/IGVFFI4478TORF/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/alignment-files/IGVFFI4478TORF/"
},
{
"category": "upload status not validated",
"detail": "Genome browser annotation file [IGVFFI4343KFGS](/genome-browser-annotation-files/IGVFFI4343KFGS/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/genome-browser-annotation-files/IGVFFI4343KFGS/"
},
{
"category": "missing input file set",
"detail": "Analysis set [IGVFDS7640LVLT](/analysis-sets/IGVFDS7640LVLT/) links to file(s) [IGVFFI4478TORF](/alignment-files/IGVFFI4478TORF/), [IGVFFI6693CTMG](/alignment-files/IGVFFI6693CTMG/) that are `derived_from` file(s) [IGVFFI0522RTLO](/model-files/IGVFFI0522RTLO/), [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/), [IGVFFI2246NBHO](/reference-files/IGVFFI2246NBHO/), [IGVFFI5402BTHV](/configuration-files/IGVFFI5402BTHV/), [IGVFFI5509NKSK](/signal-files/IGVFFI5509NKSK/), [IGVFFI4139LADO](/reference-files/IGVFFI4139LADO/), [IGVFFI6955XYXE](/signal-files/IGVFFI6955XYXE/), [IGVFFI4156PDVP](/image-files/IGVFFI4156PDVP/), [IGVFFI1190FVNM](/configuration-files/IGVFFI1190FVNM/), [IGVFFI6300KOVX](/reference-files/IGVFFI6300KOVX/), [IGVFFI2315TGLY](/reference-files/IGVFFI2315TGLY/), [IGVFFI2290GOOJ](/signal-files/IGVFFI2290GOOJ/) from file set(s) [IGVFDS5269JTLD](/curated-sets/IGVFDS5269JTLD/), [IGVFDS5330YIDV](/measurement-sets/IGVFDS5330YIDV/), [IGVFDS0280IQAI](/curated-sets/IGVFDS0280IQAI/), [IGVFDS4321MODL](/model-sets/IGVFDS4321MODL/), [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/), [IGVFDS9394DEZR](/measurement-sets/IGVFDS9394DEZR/) which are not in `input_file_sets`. The file sets of the files that are used to derive the files in an analysis set are expected to be listed in the input file sets.",
"level": 60,
"level_name": "ERROR",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/IGVFDS7640LVLT/"
},
{
"category": "upload status not validated",
"detail": "Reference file [IGVFFI2320ZTOY](/reference-files/IGVFFI2320ZTOY/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/reference-files/IGVFFI2320ZTOY/"
},
{
"category": "upload status not validated",
"detail": "Reference file [IGVFFI8327SJUS](/reference-files/IGVFFI8327SJUS/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/reference-files/IGVFFI8327SJUS/"
},
{
"category": "upload status not validated",
"detail": "Reference file [IGVFFI7352MCJK](/reference-files/IGVFFI7352MCJK/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/reference-files/IGVFFI7352MCJK/"
},
{
"category": "upload status not validated",
"detail": "Matrix file [IGVFFI2934CBSW](/matrix-files/IGVFFI2934CBSW/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/matrix-files/IGVFFI2934CBSW/"
},
{
"category": "upload status not validated",
"detail": "Reference file [IGVFFI8668BMKT](/reference-files/IGVFFI8668BMKT/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/reference-files/IGVFFI8668BMKT/"
},
{
"category": "upload status not validated",
"detail": "Reference file [IGVFFI0611SKOA](/reference-files/IGVFFI0611SKOA/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/reference-files/IGVFFI0611SKOA/"
},
{
"category": "inconsistent document type",
"detail": "Alignment file [IGVFFI6693CTMG](/alignment-files/IGVFFI6693CTMG/) has `file_format_specification` [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/) with `document_type` plasmid map. File format specifications are excepted to be documents have type file format specification.",
"level": 60,
"level_name": "ERROR",
"name": "audit_file_format_specifications",
"path": "/alignment-files/IGVFFI6693CTMG/"
},
{
"category": "upload status not validated",
"detail": "Alignment file [IGVFFI6693CTMG](/alignment-files/IGVFFI6693CTMG/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/alignment-files/IGVFFI6693CTMG/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI1347OIGI](/tabular-files/IGVFFI1347OIGI/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI1347OIGI/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS7640LVLT](/analysis-sets/IGVFDS7640LVLT/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/analysis-sets/IGVFDS7640LVLT/"
},
{
"category": "mismatched status",
"detail": "Released analysis set [IGVFDS7640LVLT](/analysis-sets/IGVFDS7640LVLT/) has in progress subobject document [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/analysis-sets/IGVFDS7640LVLT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS7640LVLT](/analysis-sets/IGVFDS7640LVLT/) links to file(s) [IGVFFI6693CTMG](/alignment-files/IGVFFI6693CTMG/), [IGVFFI4478TORF](/alignment-files/IGVFFI4478TORF/), [IGVFFI3505JBSU](/reference-files/IGVFFI3505JBSU/), [IGVFFI1347OIGI](/tabular-files/IGVFFI1347OIGI/), [IGVFFI4343KFGS](/genome-browser-annotation-files/IGVFFI4343KFGS/), [IGVFFI2934CBSW](/matrix-files/IGVFFI2934CBSW/), [IGVFFI8668BMKT](/reference-files/IGVFFI8668BMKT/), [IGVFFI7020OYZY](/reference-files/IGVFFI7020OYZY/), [IGVFFI0611SKOA](/reference-files/IGVFFI0611SKOA/), [IGVFFI7352MCJK](/reference-files/IGVFFI7352MCJK/), [IGVFFI2320ZTOY](/reference-files/IGVFFI2320ZTOY/), [IGVFFI8327SJUS](/reference-files/IGVFFI8327SJUS/) that are missing `analysis_step_version`. Analysis set files are expected to specify analysis step version.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_analysis_set_files_missing_analysis_step_version",
"path": "/analysis-sets/IGVFDS7640LVLT/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS7640LVLT](/analysis-sets/IGVFDS7640LVLT/) links to file(s) [IGVFFI3505JBSU](/reference-files/IGVFFI3505JBSU/), [IGVFFI1347OIGI](/tabular-files/IGVFFI1347OIGI/), [IGVFFI2934CBSW](/matrix-files/IGVFFI2934CBSW/), [IGVFFI8668BMKT](/reference-files/IGVFFI8668BMKT/), [IGVFFI7020OYZY](/reference-files/IGVFFI7020OYZY/), [IGVFFI0611SKOA](/reference-files/IGVFFI0611SKOA/), [IGVFFI7352MCJK](/reference-files/IGVFFI7352MCJK/), [IGVFFI2320ZTOY](/reference-files/IGVFFI2320ZTOY/), [IGVFFI8327SJUS](/reference-files/IGVFFI8327SJUS/) that have no `derived_from`. Files in an analysis set are expected to be derived from other files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/IGVFDS7640LVLT/"
},
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI2934CBSW](/matrix-files/IGVFFI2934CBSW/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/matrix-files/IGVFFI2934CBSW/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI1347OIGI](/tabular-files/IGVFFI1347OIGI/) has no `file_format_specifications`. Tabular files, with the exception of vcf files, are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI1347OIGI/"
}
]
},
"award": {
"@id": "/awards/HG012012/",
"component": "data coordination",
"title": "A Data and Administrative Coordinating Center for the Impact of Genomic Variation on Function Consortium"
},
"control_for": [],
"creation_timestamp": "2023-04-27T18:57:03.725540+00:00",
"description": "A basic analysis set we’re testing",
"documents": [
"/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/"
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI6693CTMG/",
"accession": "IGVFFI6693CTMG",
"aliases": [
"igvf:alignments_file"
],
"assembly": "GRCh38",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2023-05-24T18:20:41.817555+00:00",
"derived_from": [
"/sequence-files/IGVFFI2658WGRW/",
"/alignment-files/IGVFFI4478TORF/",
"/configuration-files/IGVFFI5402BTHV/",
"/genome-browser-annotation-files/IGVFFI4343KFGS/",
"/signal-files/IGVFFI2290GOOJ/",
"/signal-files/IGVFFI6955XYXE/",
"/tabular-files/IGVFFI1347OIGI/",
"/reference-files/IGVFFI3505JBSU/",
"/signal-files/IGVFFI5509NKSK/",
"/configuration-files/IGVFFI1190FVNM/",
"/reference-files/IGVFFI4139LADO/",
"/reference-files/IGVFFI2246NBHO/",
"/image-files/IGVFFI4156PDVP/",
"/reference-files/IGVFFI2315TGLY/",
"/model-files/IGVFFI0522RTLO/",
"/matrix-files/IGVFFI2934CBSW/",
"/reference-files/IGVFFI6300KOVX/"
],
"file_format": "bam",
"href": "/alignment-files/IGVFFI6693CTMG/@@download/IGVFFI6693CTMG.bam",
"md5sum": "7cc757ed8aacf2ec3f018876017c59c3",
"s3_uri": "s3://igvf-files-dev/2023/05/24/46e79b59-0803-46f6-b6c7-1c2533090437/IGVFFI6693CTMG.bam",
"status": "in progress",
"submitted_file_name": "/Users/igvf/path/to/alignment_file.bam",
"upload_status": "pending"
},
{
"@id": "/alignment-files/IGVFFI4478TORF/",
"accession": "IGVFFI4478TORF",
"aliases": [
"igvf:alignments_file_02"
],
"assembly": "GRCh38",
"content_type": "transcriptome alignments",
"controlled_access": false,
"creation_timestamp": "2023-05-24T18:20:43.246813+00:00",
"derived_from": [
"/sequence-files/IGVFFI2658WGRW/"
],
"file_format": "bam",
"file_size": 690000,
"href": "/alignment-files/IGVFFI4478TORF/@@download/IGVFFI4478TORF.bam",
"md5sum": "60177cc757ed8a9c41ec3f01887c9be1",
"s3_uri": "s3://igvf-files-dev/2023/05/24/f2deade7-edca-4dce-a664-5e54c14970e5/IGVFFI4478TORF.bam",
"status": "in progress",
"submitted_file_name": "/Users/igvf/path/to/alignment_file_02.bam",
"upload_status": "pending"
},
{
"@id": "/reference-files/IGVFFI3505JBSU/",
"accession": "IGVFFI3505JBSU",
"assembly": "GRCh38",
"content_type": "genomic_elements",
"controlled_access": false,
"creation_timestamp": "2023-05-08T17:16:35.243926+00:00",
"file_format": "fasta",
"href": "/reference-files/IGVFFI3505JBSU/@@download/IGVFFI3505JBSU.fasta.gz",
"md5sum": "7f1917dea86105dd9d2582c0a91c3154",
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"status": "in progress",
"submitted_file_name": "/users/path/to/reference_file.fasta",
"upload_status": "pending"
},
{
"@id": "/tabular-files/IGVFFI1347OIGI/",
"accession": "IGVFFI1347OIGI",
"aliases": [
"igvf:example_tabular_file_01"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2023-12-05T01:54:17.472843+00:00",
"file_format": "bed",
"href": "/tabular-files/IGVFFI1347OIGI/@@download/IGVFFI1347OIGI.bed.gz",
"md5sum": "c9be16849c41ecc5c7ed8af9502358c7",
"s3_uri": "s3://igvf-files-dev/2023/12/05/87a4e906-a377-4034-90f1-9fee7eeae269/IGVFFI1347OIGI.bed.gz",
"status": "in progress",
"submitted_file_name": "/path/to/tabular_file.bed",
"transcriptome_annotation": "GENCODE 40",
"upload_status": "pending"
},
{
"@id": "/genome-browser-annotation-files/IGVFFI4343KFGS/",
"accession": "IGVFFI4343KFGS",
"aliases": [
"igvf:example_genome_browser_annotation_file_01"
],
"assembly": "GRCh38",
"content_type": "peaks",
"creation_timestamp": "2023-12-05T01:56:54.518413+00:00",
"derived_from": [
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],
"file_format": "bigBed",
"file_size": 50000000,
"href": "/genome-browser-annotation-files/IGVFFI4343KFGS/@@download/IGVFFI4343KFGS.bigBed",
"md5sum": "1c4839acd8c91ec23247c80a850f5e5e",
"s3_uri": "s3://igvf-files-dev/2023/12/05/b99c9219-cccf-4d23-b35c-1dbd1f3b6fcd/IGVFFI4343KFGS.bigBed",
"status": "in progress",
"submitted_file_name": "/path/to/visualizable_peaks.bigBed",
"transcriptome_annotation": "GENCODE 40",
"upload_status": "pending"
},
{
"@id": "/matrix-files/IGVFFI2934CBSW/",
"accession": "IGVFFI2934CBSW",
"aliases": [
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],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2023-09-19T21:38:29.606787+00:00",
"file_format": "h5ad",
"href": "/matrix-files/IGVFFI2934CBSW/@@download/IGVFFI2934CBSW.h5ad",
"md5sum": "1fa7f11eb56d045ee0aea2d92fbd1217",
"s3_uri": "s3://igvf-files-dev/2023/09/19/3c04ce38-18ef-4a44-a6a7-eb514c6f0556/IGVFFI2934CBSW.h5ad",
"status": "in progress",
"submitted_file_name": "/path/to/matrix_file.h5ad",
"upload_status": "pending"
},
{
"@id": "/reference-files/IGVFFI8668BMKT/",
"accession": "IGVFFI8668BMKT",
"assembly": "GRCh38",
"content_type": "genomic_elements_genes",
"controlled_access": false,
"creation_timestamp": "2025-02-24T16:40:27.954412+00:00",
"file_format": "fasta",
"href": "/reference-files/IGVFFI8668BMKT/@@download/IGVFFI8668BMKT.fasta.gz",
"md5sum": "d8c1e1b377534e0338d15286e3d22eea",
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"status": "in progress",
"upload_status": "pending"
},
{
"@id": "/reference-files/IGVFFI7020OYZY/",
"accession": "IGVFFI7020OYZY",
"assembly": "GRCh38",
"content_type": "genomic_elements_genes_biosamples",
"controlled_access": false,
"creation_timestamp": "2025-02-24T16:41:18.733377+00:00",
"file_format": "fasta",
"href": "/reference-files/IGVFFI7020OYZY/@@download/IGVFFI7020OYZY.fasta.gz",
"md5sum": "5ae7f9ddfc558b27f25fa81adee24912",
"s3_uri": "s3://igvf-files-dev/2025/02/24/483d4ef3-e4fb-437d-ad93-2c37343cbedb/IGVFFI7020OYZY.fasta.gz",
"status": "in progress",
"upload_status": "pending"
},
{
"@id": "/reference-files/IGVFFI0611SKOA/",
"accession": "IGVFFI0611SKOA",
"assembly": "GRCh38",
"content_type": "genomic_elements_genes_biosamples_donors",
"controlled_access": false,
"creation_timestamp": "2025-02-24T16:43:12.015264+00:00",
"file_format": "fasta",
"href": "/reference-files/IGVFFI0611SKOA/@@download/IGVFFI0611SKOA.fasta.gz",
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"status": "in progress",
"upload_status": "pending"
},
{
"@id": "/reference-files/IGVFFI7352MCJK/",
"accession": "IGVFFI7352MCJK",
"assembly": "GRCh38",
"content_type": "genomic_elements_genes_biosamples_treatments_chebi",
"controlled_access": false,
"creation_timestamp": "2025-02-24T16:43:56.091970+00:00",
"file_format": "fasta",
"href": "/reference-files/IGVFFI7352MCJK/@@download/IGVFFI7352MCJK.fasta.gz",
"md5sum": "ae96f6ec12169c5b2c9271da9b946ad8",
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"status": "in progress",
"upload_status": "pending"
},
{
"@id": "/reference-files/IGVFFI2320ZTOY/",
"accession": "IGVFFI2320ZTOY",
"assembly": "GRCh38",
"content_type": "genomic_elements_genomic_elements",
"controlled_access": false,
"creation_timestamp": "2025-02-24T16:47:26.564933+00:00",
"file_format": "fasta",
"href": "/reference-files/IGVFFI2320ZTOY/@@download/IGVFFI2320ZTOY.fasta.gz",
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"status": "in progress",
"upload_status": "pending"
},
{
"@id": "/reference-files/IGVFFI8327SJUS/",
"accession": "IGVFFI8327SJUS",
"assembly": "GRCh38",
"content_type": "genomic_elements_genes_biosamples_treatments_proteins",
"controlled_access": false,
"creation_timestamp": "2025-02-24T16:44:56.164847+00:00",
"file_format": "fasta",
"href": "/reference-files/IGVFFI8327SJUS/@@download/IGVFFI8327SJUS.fasta.gz",
"md5sum": "d41858222dcf4aa19e0e5b98c0dcc699",
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"status": "in progress",
"upload_status": "pending"
}
],
"functional_assay_mechanisms": [],
"input_for": [
"/analysis-sets/IGVFDS4435CQCE/"
],
"lab": {
"@id": "/labs/j-michael-cherry/",
"title": "J. Michael Cherry, Stanford"
},
"notes": ". This analysis set previous specified samples: /tissues/IGVFSM3939SHHK/, but this property is now calculated through the input_file_sets.",
"protocols": [],
"release_timestamp": "2023-04-27T18:57:03.706525+00:00",
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/1e75d989-a438-4d77-a451-8a297fd3636e/",
"title": "Ian Whaling"
},
"submitted_files_timestamp": "2023-05-08T17:16:35.243926+00:00",
"submitter_comment": "Comment for an analysis set.",
"summary": "Unspecified assay: alignments, genomic_elements, genomic_elements_genes, genomic_elements_genes_biosamples, genomic_elements_genes_biosamples_donors and 6 more",
"uuid": "6d0717f6-cb4f-4e97-9b65-5ca0ced173d3",
"workflows": []
}