IGVFFI9504YUXH

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI9504YUXH/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI9504YUXH",
10    "aliases": [
11        "ansuman-satpathy:igvf6_peaks_10x1"
12    ],
13    "analysis_step_version": "/analysis-step-versions/699d6738-4033-4afc-b6f3-1d82a80e0b41/",
14    "assay_titles": [
15        "10x multiome with MULTI-seq"
16    ],
17    "assembly": "GRCh38",
18    "audit": {},
19    "award": {
20        "@id": "/awards/HG011972/",
21        "component": "functional characterization"
22    },
23    "barcode_map_for": [],
24    "checkfiles_version": "v14",
25    "content_md5sum": "6cd76325a4f252c48e60408cb696ce0f",
26    "content_type": "peaks",
27    "controlled_access": false,
28    "creation_timestamp": "2025-01-28T05:58:30.945347+00:00",
29    "derived_from": [
30        "/tabular-files/IGVFFI9475IAXV/"
31    ],
32    "file_format": "bed",
33    "file_format_specifications": [
34        {
35            "@id": "/documents/07404908-2ed4-4286-8345-97e0fc205b36/",
36            "description": "10X Genomics Peaks Bedfile"
37        }
38    ],
39    "file_format_type": "bed3",
40    "file_set": {
41        "@id": "/analysis-sets/IGVFDS3232NVVG/",
42        "@type": [
43            "AnalysisSet",
44            "FileSet",
45            "Item"
46        ],
47        "accession": "IGVFDS3232NVVG",
48        "controlled_access": false,
49        "data_use_limitation_summaries": [
50            "No limitations"
51        ],
52        "file_set_type": "intermediate analysis",
53        "samples": [
54            {
55                "@id": "/multiplexed-samples/IGVFSM9282FATG/",
56                "@type": [
57                    "MultiplexedSample",
58                    "Sample",
59                    "Item"
60                ],
61                "accession": "IGVFSM9282FATG",
62                "classifications": [
63                    "cell line",
64                    "differentiated cell specimen",
65                    "multiplexed sample"
66                ],
67                "disease_terms": [],
68                "modifications": [],
69                "sample_terms": [
70                    {
71                        "@id": "/sample-terms/EFO_0003042/",
72                        "status": "released",
73                        "term_name": "H1-hESC"
74                    }
75                ],
76                "status": "released",
77                "summary": "multiplexed sample: Homo sapiens (male) H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days; Homo sapiens (male) H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 days; ... and 6 more samples",
78                "taxa": "Homo sapiens",
79                "treatments": []
80            }
81        ],
82        "status": "released",
83        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
84    },
85    "file_size": 2429810,
86    "gene_list_for": [],
87    "href": "/tabular-files/IGVFFI9504YUXH/@@download/IGVFFI9504YUXH.bed.gz",
88    "input_file_for": [],
89    "integrated_in": [],
90    "lab": {
91        "@id": "/labs/ansuman-satpathy/",
92        "title": "Ansuman Satpathy, Stanford"
93    },
94    "loci_list_for": [],
95    "md5sum": "5dcd936102cb943f6e19ddf1688796a1",
96    "primer_design_for": [],
97    "quality_metrics": [],
98    "release_timestamp": "2025-03-07T06:04:45.970833+00:00",
99    "s3_uri": "s3://igvf-files/2025/01/28/c495903f-f7b0-42d0-83c0-9069fd2bf215/IGVFFI9504YUXH.bed.gz",
100    "schema_version": "15",
101    "status": "released",
102    "submitted_by": {
103        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
104        "title": "Christopher Mcginnis"
105    },
106    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l1_peaks.bed",
107    "summary": "GRCh38 peaks",
108    "upload_status": "validation exempted",
109    "uuid": "c495903f-f7b0-42d0-83c0-9069fd2bf215",
110    "validation_error_detail": "{\"md5sum\": \"original md5sum 6cd76325a4f252c48e60408cb696ce0f does not match newly calculated md5sum 5dcd936102cb943f6e19ddf1688796a1.\", \"validate_files\": \"Error [file=/home/ubuntu/igvf-files/2025/01/28/c495903f-f7b0-42d0-83c0-9069fd2bf215/IGVFFI9504YUXH.bed.gz, line=295671]: chrom KI270728.1 not found [KI270728.1\\t232289\\t233191]\\nAborting ... found error.\"}",
111    "workflow": {
112        "@id": "/workflows/IGVFWF1453HVEC/",
113        "name": "Satpathy Cell Ranger",
114        "uniform_pipeline": false
115    }
116}