{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS7640LVLT/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7640LVLT",
"aliases": [
"igvf:s"
],
"audit": {
"ERROR": [
{
"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": "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/"
},
{
"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": "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": "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": "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": "missing input file set",
"detail": "Analysis set [IGVFDS7640LVLT](/analysis-sets/IGVFDS7640LVLT/) links to file(s) [IGVFFI6693CTMG](/alignment-files/IGVFFI6693CTMG/), [IGVFFI4478TORF](/alignment-files/IGVFFI4478TORF/) that are `derived_from` file(s) [IGVFFI4139LADO](/reference-files/IGVFFI4139LADO/), [IGVFFI4156PDVP](/image-files/IGVFFI4156PDVP/), [IGVFFI2246NBHO](/reference-files/IGVFFI2246NBHO/), [IGVFFI0522RTLO](/model-files/IGVFFI0522RTLO/), [IGVFFI6300KOVX](/reference-files/IGVFFI6300KOVX/), [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/), [IGVFFI5509NKSK](/signal-files/IGVFFI5509NKSK/), [IGVFFI2315TGLY](/reference-files/IGVFFI2315TGLY/), [IGVFFI5402BTHV](/configuration-files/IGVFFI5402BTHV/), [IGVFFI6955XYXE](/signal-files/IGVFFI6955XYXE/), [IGVFFI2290GOOJ](/signal-files/IGVFFI2290GOOJ/), [IGVFFI1190FVNM](/configuration-files/IGVFFI1190FVNM/) from file set(s) [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/), [IGVFDS5330YIDV](/measurement-sets/IGVFDS5330YIDV/), [IGVFDS0280IQAI](/curated-sets/IGVFDS0280IQAI/), [IGVFDS5269JTLD](/curated-sets/IGVFDS5269JTLD/), [IGVFDS9394DEZR](/measurement-sets/IGVFDS9394DEZR/), [IGVFDS4321MODL](/model-sets/IGVFDS4321MODL/) 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/"
}
],
"INTERNAL_ACTION": [
{
"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 file format specifications",
"detail": "Tabular file [IGVFFI1347OIGI](/tabular-files/IGVFFI1347OIGI/) has no `file_format_specifications`. Tabular 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/"
},
{
"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 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/) 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/) 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/"
}
]
},
"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",
"file_format": "bam",
"href": "/alignment-files/IGVFFI6693CTMG/@@download/IGVFFI6693CTMG.bam",
"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",
"file_format": "bam",
"file_size": 690000,
"href": "/alignment-files/IGVFFI4478TORF/@@download/IGVFFI4478TORF.bam",
"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": "genome reference",
"controlled_access": false,
"creation_timestamp": "2023-05-08T17:16:35.243926+00:00",
"file_format": "fasta",
"href": "/reference-files/IGVFFI3505JBSU/@@download/IGVFFI3505JBSU.fasta.gz",
"s3_uri": "s3://igvf-files-dev/2023/05/08/7d772517-dbfa-4f5c-8282-4c7ad8004704/IGVFFI3505JBSU.fasta.gz",
"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",
"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",
"file_format": "bigBed",
"file_size": 50000000,
"href": "/genome-browser-annotation-files/IGVFFI4343KFGS/@@download/IGVFFI4343KFGS.bigBed",
"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": [
"igvf:example_matrix_file_01"
],
"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",
"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"
}
],
"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, genome reference, peaks, sparse gene count matrix, transcriptome alignments",
"uuid": "6d0717f6-cb4f-4e97-9b65-5ca0ced173d3",
"workflows": []
}