IGVFFI4907GYFZ

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI4907GYFZ/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI4907GYFZ",
10    "aliases": [
11        "ansuman-satpathy:igvf9_fragments_10x2"
12    ],
13    "analysis_step_version": "/analysis-step-versions/4e4a3f0b-c3bc-477c-bc53-c3091bc56756/",
14    "assay_titles": [
15        "10x multiome with MULTI-seq"
16    ],
17    "audit": {},
18    "award": {
19        "@id": "/awards/HG011972/",
20        "component": "functional characterization"
21    },
22    "barcode_map_for": [],
23    "checkfiles_version": "v14",
24    "content_md5sum": "2cde63ec29dcf22ccc59309e55fdc328",
25    "content_type": "fragments",
26    "controlled_access": true,
27    "creation_timestamp": "2025-01-28T06:02:33.757635+00:00",
28    "derived_from": [
29        "/sequence-files/IGVFFI9247KOVT/",
30        "/sequence-files/IGVFFI0270TTFC/",
31        "/sequence-files/IGVFFI4857JZLI/",
32        "/sequence-files/IGVFFI0126DWYC/",
33        "/sequence-files/IGVFFI0060PNZQ/",
34        "/sequence-files/IGVFFI4991KQMH/",
35        "/sequence-files/IGVFFI2875ZLRI/",
36        "/sequence-files/IGVFFI5847LLGI/",
37        "/sequence-files/IGVFFI8123QWYG/",
38        "/sequence-files/IGVFFI8454EASP/",
39        "/sequence-files/IGVFFI4156JJZJ/",
40        "/sequence-files/IGVFFI8332QYKO/"
41    ],
42    "file_format": "tsv",
43    "file_format_specifications": [
44        "/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
45    ],
46    "file_set": {
47        "@id": "/analysis-sets/IGVFDS6435ALNY/",
48        "@type": [
49            "AnalysisSet",
50            "FileSet",
51            "Item"
52        ],
53        "accession": "IGVFDS6435ALNY",
54        "file_set_type": "intermediate analysis",
55        "samples": [
56            {
57                "@id": "/multiplexed-samples/IGVFSM2512OHNK/",
58                "@type": [
59                    "MultiplexedSample",
60                    "Sample",
61                    "Item"
62                ],
63                "accession": "IGVFSM2512OHNK",
64                "classifications": [
65                    "differentiated cell specimen",
66                    "multiplexed sample"
67                ],
68                "disease_terms": [],
69                "modifications": [],
70                "sample_terms": [
71                    {
72                        "@id": "/sample-terms/CL_0000236/",
73                        "status": "released",
74                        "term_name": "B cell"
75                    }
76                ],
77                "status": "released",
78                "summary": "multiplexed sample: Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 1 day; Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 5 days; ... and 5 more samples",
79                "taxa": "Homo sapiens",
80                "treatments": []
81            }
82        ],
83        "status": "released",
84        "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
85    },
86    "file_size": 6639939248,
87    "gene_list_for": [],
88    "href": "/tabular-files/IGVFFI4907GYFZ/@@download/IGVFFI4907GYFZ.tsv.gz",
89    "input_file_for": [
90        "/index-files/IGVFFI7725ECTZ/",
91        "/tabular-files/IGVFFI5180HSIX/"
92    ],
93    "integrated_in": [],
94    "lab": {
95        "@id": "/labs/ansuman-satpathy/",
96        "title": "Ansuman Satpathy, Stanford"
97    },
98    "loci_list_for": [],
99    "md5sum": "d82c0730a021ef69b13197aa04208a4a",
100    "notes": "File has # in headers, the current version of checkfiles does not allow for that but this is a valid file output from cell ranger. Therefore, we have patched the upload_status to \"validation exempted\"",
101    "quality_metrics": [],
102    "release_timestamp": "2025-03-22T00:42:52.800771+00:00",
103    "s3_uri": "s3://igvf-restricted-files/2025/01/28/6a7eef64-4e21-4b74-9cec-11ad77579632/IGVFFI4907GYFZ.tsv.gz",
104    "schema_version": "15",
105    "status": "released",
106    "submitted_by": {
107        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
108        "title": "Christopher Mcginnis"
109    },
110    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l2_fragments.tsv.gz",
111    "summary": "fragments",
112    "upload_status": "validation exempted",
113    "uuid": "6a7eef64-4e21-4b74-9cec-11ad77579632",
114    "validation_error_detail": "{\"tabular_file_error\": {\"schema\": null, \"error_number_limit\": 1000, \"number_of_errors\": 1000, \"extra-cell\": {\"count\": 1000, \"description\": \"This row has more values compared to the header row (the first row in the data source). A key concept is that all the rows in tabular data must have the same number of columns.\", \"details\": [{\"row_number\": 52, \"field_number\": 2, \"note\": \"\"}, {\"row_number\": 52, \"field_number\": 3, \"note\": \"\"}]}, \"error_types\": [\"extra-cell\"]}}",
115    "workflow": {
116        "@id": "/workflows/IGVFWF1453HVEC/",
117        "name": "Satpathy Cell Ranger",
118        "uniform_pipeline": false
119    }
120}