| { |
| "schema": "bench_h2h real-data downloads v1", |
| "written_utc": "2026-09-15T15:40:13Z", |
| "actor": "download", |
| "approval": { |
| "text": "批准，先跑我们的模型，快速的先出一个结果我看看", |
| "by": "Larry", |
| "date": "2026-09-15", |
| "relayed_by": "orchestrator (real-data quick-look task prompt)" |
| }, |
| "scope_rule": "ONLY these files may be downloaded for the real-data quick look (no other chromosomes, no Ensembl ancestor, no other maps)", |
| "method": { |
| "host": "login509-02-r (Ibex login node), single stream, sequential", |
| "head": "curl -sS -I -L --retry 5 --retry-delay 10 URL > headers/<basename>.headers", |
| "get": "curl -sS -L --fail --retry 20 --retry-delay 15 --retry-connrefused -C - -o <dest> URL", |
| "checks": "HEAD Content-Length == approved bytes (refuse otherwise; tbi: HEAD only); bytes on disk == Content-Length; sha256sum of the on-disk file; chmod a-w", |
| "script": "real/scripts/download_real.sh", |
| "script_sha256": "6317c061817c4e8b8ef858b0cea9a6e2d023aba6819ba1043905a17bff64c12a", |
| "log": "real/logs/download.log", |
| "log_sha256": "fd161c4452d387c3602ba85afcf3801c14f1e59fda7bcddaff54013c5b887dbd" |
| }, |
| "files": [ |
| { |
| "name": "ped", |
| "url": "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/20130606_g1k_3202_samples_ped_population.txt", |
| "path": "real/ref/20130606_g1k_3202_samples_ped_population.txt", |
| "approval_basis": "quick-look approval 2026-09-15", |
| "approved_bytes": 97483, |
| "head": { |
| "status_line": "HTTP/1.1 200 OK", |
| "date": "Tue, 15 Sep 2026 14:16:52 GMT", |
| "server": "Apache", |
| "last-modified": "Mon, 25 May 2020 14:14:09 GMT", |
| "etag": "\"17ccb-5a67997a54e40\"", |
| "accept-ranges": "bytes", |
| "content-length": "97483", |
| "content-type": "text/plain; charset=UTF-8" |
| }, |
| "headers_file": "real/headers/20130606_g1k_3202_samples_ped_population.txt.headers", |
| "bytes": 97483, |
| "content_length_match": true, |
| "sha256": "4e164b717433fc9bfc16e29b20e5b4659b4216185b3275322d421fe3d323c132", |
| "sha256_sidecar": "real/ref/20130606_g1k_3202_samples_ped_population.txt.sha256", |
| "head_utc": "2026-09-15T14:16:52Z", |
| "done_utc": "2026-09-15T14:16:59Z", |
| "mode": "0o444" |
| }, |
| { |
| "name": "gap", |
| "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/gap.txt.gz", |
| "path": "real/ref/gap.txt.gz", |
| "approval_basis": "T0 (previously approved)", |
| "approved_bytes": 12368, |
| "head": { |
| "status_line": "HTTP/1.1 200 OK", |
| "date": "Tue, 15 Sep 2026 14:17:01 GMT", |
| "server": "Apache", |
| "last-modified": "Wed, 19 Oct 2022 06:39:31 GMT", |
| "etag": "\"3050-5eb5d78a1c1dc\"", |
| "accept-ranges": "bytes", |
| "content-length": "12368", |
| "content-type": "application/x-gzip" |
| }, |
| "headers_file": "real/headers/gap.txt.gz.headers", |
| "bytes": 12368, |
| "content_length_match": true, |
| "sha256": "c466135bf8553f007960b3bd7d747343d014143a0415c127d1452bbe484bf1c1", |
| "sha256_sidecar": "real/ref/gap.txt.gz.sha256", |
| "head_utc": "2026-09-15T14:17:01Z", |
| "done_utc": "2026-09-15T14:17:02Z", |
| "mode": "0o444" |
| }, |
| { |
| "name": "centromeres", |
| "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/centromeres.txt.gz", |
| "path": "real/ref/centromeres.txt.gz", |
| "approval_basis": "T0 (previously approved)", |
| "approved_bytes": 1549, |
| "head": { |
| "status_line": "HTTP/1.1 200 OK", |
| "date": "Tue, 15 Sep 2026 14:17:03 GMT", |
| "server": "Apache", |
| "last-modified": "Sun, 17 Aug 2014 19:08:51 GMT", |
| "etag": "\"60d-500d7fc18b6c0\"", |
| "accept-ranges": "bytes", |
| "content-length": "1549", |
| "content-type": "application/x-gzip" |
| }, |
| "headers_file": "real/headers/centromeres.txt.gz.headers", |
| "bytes": 1549, |
| "content_length_match": true, |
| "sha256": "013c8d165402908f7c9e6de7860534fad2c85ac75e9dd2127166a23b06cac3bd", |
| "sha256_sidecar": "real/ref/centromeres.txt.gz.sha256", |
| "head_utc": "2026-09-15T14:17:03Z", |
| "done_utc": "2026-09-15T14:17:04Z", |
| "mode": "0o444" |
| }, |
| { |
| "name": "pilot_mask", |
| "url": "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/working/20160622_genome_mask_GRCh38/PilotMask/20160622.allChr.pilot_mask.bed", |
| "path": "real/ref/20160622.allChr.pilot_mask.bed", |
| "approval_basis": "T0 (previously approved)", |
| "approved_bytes": 16728941, |
| "head": { |
| "status_line": "HTTP/1.1 200 OK", |
| "date": "Tue, 15 Sep 2026 14:17:05 GMT", |
| "server": "Apache", |
| "last-modified": "Wed, 22 Jun 2016 15:55:33 GMT", |
| "etag": "\"ff436d-535dff7af6740\"", |
| "accept-ranges": "bytes", |
| "content-length": "16728941", |
| "content-type": "application/vnd.realvnc.bed" |
| }, |
| "headers_file": "real/headers/20160622.allChr.pilot_mask.bed.headers", |
| "bytes": 16728941, |
| "content_length_match": true, |
| "sha256": "2bf938e847639c582bda748613b9a5080577d5633fd8fa9f44086eedc608d22d", |
| "sha256_sidecar": "real/ref/20160622.allChr.pilot_mask.bed.sha256", |
| "head_utc": "2026-09-15T14:17:05Z", |
| "done_utc": "2026-09-15T14:17:39Z", |
| "mode": "0o444" |
| }, |
| { |
| "name": "strict_mask", |
| "url": "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/working/20160622_genome_mask_GRCh38/StrictMask/20160622.allChr.mask.bed", |
| "path": "real/ref/20160622.allChr.mask.bed", |
| "approval_basis": "T0 (previously approved)", |
| "approved_bytes": 128218530, |
| "head": { |
| "status_line": "HTTP/1.1 200 OK", |
| "date": "Tue, 15 Sep 2026 14:17:40 GMT", |
| "server": "Apache", |
| "last-modified": "Wed, 22 Jun 2016 15:54:27 GMT", |
| "etag": "\"7a475a2-535dff3c052c0\"", |
| "accept-ranges": "bytes", |
| "content-length": "128218530", |
| "content-type": "application/vnd.realvnc.bed" |
| }, |
| "headers_file": "real/headers/20160622.allChr.mask.bed.headers", |
| "bytes": 128218530, |
| "content_length_match": true, |
| "sha256": "c40df20a1f55dca85152985bdd52e5a27857b317c18193a24dbae860d2c5b46f", |
| "sha256_sidecar": "real/ref/20160622.allChr.mask.bed.sha256", |
| "head_utc": "2026-09-15T14:17:40Z", |
| "done_utc": "2026-09-15T14:22:29Z", |
| "mode": "0o444" |
| }, |
| { |
| "name": "vcf_tbi", |
| "url": "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz.tbi", |
| "path": "real/raw/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz.tbi", |
| "approval_basis": "quick-look approval 2026-09-15 (tbi named as part of the approval; size taken from HEAD)", |
| "approved_bytes": null, |
| "head": { |
| "status_line": "HTTP/1.1 200 OK", |
| "date": "Tue, 15 Sep 2026 14:22:30 GMT", |
| "server": "Apache", |
| "last-modified": "Mon, 25 Apr 2022 14:26:00 GMT", |
| "etag": "\"2f677-5dd7b5af0ce00\"", |
| "accept-ranges": "bytes", |
| "content-length": "194167", |
| "content-type": "application/x-gzip" |
| }, |
| "headers_file": "real/headers/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz.tbi.headers", |
| "bytes": 194167, |
| "content_length_match": true, |
| "sha256": "e47ca9e6200d4be17792f79582bf5754d3810c04be3f6834f35a9fc688d8478f", |
| "sha256_sidecar": "real/raw/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz.tbi.sha256", |
| "head_utc": "2026-09-15T14:22:30Z", |
| "done_utc": "2026-09-15T14:22:32Z", |
| "mode": "0o444" |
| }, |
| { |
| "name": "vcf", |
| "url": "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz", |
| "path": "real/raw/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz", |
| "approval_basis": "quick-look approval 2026-09-15", |
| "approved_bytes": 2506332497, |
| "head": { |
| "status_line": "HTTP/1.1 200 OK", |
| "date": "Tue, 15 Sep 2026 14:22:32 GMT", |
| "server": "Apache", |
| "last-modified": "Mon, 25 Apr 2022 15:17:57 GMT", |
| "etag": "\"95639951-5dd7c14ba7340\"", |
| "accept-ranges": "bytes", |
| "content-length": "2506332497", |
| "content-type": "application/x-gzip" |
| }, |
| "headers_file": "real/headers/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz.headers", |
| "bytes": 2506332497, |
| "content_length_match": true, |
| "sha256": "9c82055d2a5dde853ea379fa1c2ccbb467639abd6fcd8b96b3a138d05e39cab7", |
| "sha256_sidecar": "real/raw/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz.sha256", |
| "head_utc": "2026-09-15T14:22:32Z", |
| "done_utc": "2026-09-15T15:04:46Z", |
| "mode": "0o444" |
| } |
| ], |
| "copies": [ |
| { |
| "name": "decode2019_avg_hg38", |
| "source": "laptop:/Users/larryivanhan/Desktop/Projects/genomics/DLCoal/maps/recomb_map/output/decode2019_avg_hg38.bed", |
| "source_sha256": "1a61cd217c48fff272671885c06f9f8b4018e30bffbe54031ba0b82d392a3c17", |
| "path": "real/ref/decode2019_avg_hg38.bed", |
| "bytes": 20815651, |
| "sha256": "1a61cd217c48fff272671885c06f9f8b4018e30bffbe54031ba0b82d392a3c17", |
| "sha_match": true, |
| "mode": "0o444", |
| "note": "local copy, not a download; built by maps/recomb_map/build_decode2019.py" |
| } |
| ] |
| } |
|
|
