IGVFFI6774RPHJ

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI6774RPHJ/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI6774RPHJ",
10    "aliases": [
11        "ansuman-satpathy:igvf2_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": "ef39a86dabd7b963e242b846c256d28b",
25    "content_type": "fragments",
26    "controlled_access": false,
27    "creation_timestamp": "2025-01-28T05:49:52.696812+00:00",
28    "derived_from": [
29        "/sequence-files/IGVFFI0553QQBA/",
30        "/sequence-files/IGVFFI2670GFYR/",
31        "/sequence-files/IGVFFI4050ZLEP/",
32        "/sequence-files/IGVFFI8043XYMX/",
33        "/sequence-files/IGVFFI2547LRAU/",
34        "/sequence-files/IGVFFI9291YSSU/",
35        "/sequence-files/IGVFFI3640SGYN/",
36        "/sequence-files/IGVFFI0491OLML/"
37    ],
38    "file_format": "tsv",
39    "file_format_specifications": [
40        "/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
41    ],
42    "file_set": {
43        "@id": "/analysis-sets/IGVFDS1583PWNS/",
44        "@type": [
45            "AnalysisSet",
46            "FileSet",
47            "Item"
48        ],
49        "accession": "IGVFDS1583PWNS",
50        "file_set_type": "intermediate analysis",
51        "samples": [
52            {
53                "@id": "/multiplexed-samples/IGVFSM3646QLDO/",
54                "@type": [
55                    "MultiplexedSample",
56                    "Sample",
57                    "Item"
58                ],
59                "accession": "IGVFSM3646QLDO",
60                "classifications": [
61                    "cell line",
62                    "multiplexed sample"
63                ],
64                "disease_terms": [],
65                "modifications": [],
66                "sample_terms": [
67                    {
68                        "@id": "/sample-terms/NTR_0000753/",
69                        "status": "released",
70                        "term_name": "TeloHAEC"
71                    }
72                ],
73                "status": "released",
74                "summary": "multiplexed sample: Homo sapiens (female) TeloHAEC cell line treated with 10 ng/mL tumor necrosis factor alpha for 4 hours; Homo sapiens (female) TeloHAEC cell line; ... and 7 more samples",
75                "taxa": "Homo sapiens",
76                "treatments": [
77                    {
78                        "@id": "/treatments/d2d49540-dd91-49e2-b877-ce9aa0af8bb0/",
79                        "purpose": "perturbation",
80                        "status": "in progress",
81                        "summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 4 hours",
82                        "treatment_term_name": "tumor necrosis factor alpha"
83                    },
84                    {
85                        "@id": "/treatments/de8a9e87-d0e1-4ecb-bc9d-08e61b4ff368/",
86                        "purpose": "perturbation",
87                        "status": "in progress",
88                        "summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 1 day",
89                        "treatment_term_name": "tumor necrosis factor alpha"
90                    }
91                ]
92            }
93        ],
94        "status": "released",
95        "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
96    },
97    "file_size": 6902347644,
98    "gene_list_for": [],
99    "href": "/tabular-files/IGVFFI6774RPHJ/@@download/IGVFFI6774RPHJ.tsv.gz",
100    "input_file_for": [
101        "/index-files/IGVFFI3495CSEB/",
102        "/tabular-files/IGVFFI3993MUKU/"
103    ],
104    "integrated_in": [],
105    "lab": {
106        "@id": "/labs/ansuman-satpathy/",
107        "title": "Ansuman Satpathy, Stanford"
108    },
109    "loci_list_for": [],
110    "md5sum": "c46d281cd46957f1f56476ce3326be6f",
111    "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\"",
112    "quality_metrics": [],
113    "release_timestamp": "2025-03-07T06:04:09.313178+00:00",
114    "s3_uri": "s3://igvf-files/2025/01/28/a7f47513-3365-43cb-9638-06af30ce84bf/IGVFFI6774RPHJ.tsv.gz",
115    "schema_version": "15",
116    "status": "released",
117    "submitted_by": {
118        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
119        "title": "Christopher Mcginnis"
120    },
121    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf2/e2l1_fragments.tsv.gz",
122    "summary": "fragments",
123    "upload_status": "validation exempted",
124    "uuid": "a7f47513-3365-43cb-9638-06af30ce84bf",
125    "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\"]}}",
126    "workflow": {
127        "@id": "/workflows/IGVFWF1453HVEC/",
128        "name": "Satpathy Cell Ranger",
129        "uniform_pipeline": false
130    }
131}