IGVFFI6893BJEL

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI6893BJEL/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI6893BJEL",
10    "aliases": [
11        "ansuman-satpathy:igvf9_fragments_10x1"
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": "23cdb674a10fbbb666b32904c654d50f",
25    "content_type": "fragments",
26    "controlled_access": true,
27    "creation_timestamp": "2025-01-28T06:01:41.804679+00:00",
28    "derived_from": [
29        "/sequence-files/IGVFFI8765ADYG/",
30        "/sequence-files/IGVFFI4771BNJQ/",
31        "/sequence-files/IGVFFI4081VDFX/",
32        "/sequence-files/IGVFFI0239TWOF/",
33        "/sequence-files/IGVFFI6559YOVP/",
34        "/sequence-files/IGVFFI4530QVSQ/",
35        "/sequence-files/IGVFFI7980UOIM/",
36        "/sequence-files/IGVFFI4103OUZF/",
37        "/sequence-files/IGVFFI1173NUWO/",
38        "/sequence-files/IGVFFI2878FVGO/",
39        "/sequence-files/IGVFFI2587RPQQ/",
40        "/sequence-files/IGVFFI2207GMOH/"
41    ],
42    "file_format": "tsv",
43    "file_format_specifications": [
44        "/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
45    ],
46    "file_set": {
47        "@id": "/analysis-sets/IGVFDS7527QIIX/",
48        "@type": [
49            "AnalysisSet",
50            "FileSet",
51            "Item"
52        ],
53        "accession": "IGVFDS7527QIIX",
54        "file_set_type": "intermediate analysis",
55        "samples": [
56            {
57                "@id": "/multiplexed-samples/IGVFSM9678IFHW/",
58                "@type": [
59                    "MultiplexedSample",
60                    "Sample",
61                    "Item"
62                ],
63                "accession": "IGVFSM9678IFHW",
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": 6275922375,
87    "gene_list_for": [],
88    "href": "/tabular-files/IGVFFI6893BJEL/@@download/IGVFFI6893BJEL.tsv.gz",
89    "input_file_for": [
90        "/index-files/IGVFFI3282WWBA/",
91        "/tabular-files/IGVFFI1533ZRUW/"
92    ],
93    "integrated_in": [],
94    "lab": {
95        "@id": "/labs/ansuman-satpathy/",
96        "title": "Ansuman Satpathy, Stanford"
97    },
98    "loci_list_for": [],
99    "md5sum": "5db3fae19bc4f1bc9ac9a8ad1e653023",
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": "2025-03-22T00:41:39.789806+00:00",
103    "s3_uri": "s3://igvf-restricted-files/2025/01/28/53dbc753-4120-46d6-a75e-a4e179ae8a50/IGVFFI6893BJEL.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/e9l1_fragments.tsv.gz",
111    "summary": "fragments",
112    "upload_status": "validation exempted",
113    "uuid": "53dbc753-4120-46d6-a75e-a4e179ae8a50",
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}