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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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Missing LD files #178

Closed kkupkova closed 8 months ago

kkupkova commented 8 months ago

Hi,

I wanted to use your generated LD matrices but I am running into problems with few of the files. The regions below seem to have only .gz file, but the .npz file.

chr6_26000001_29000001 chr6_27000001_30000001 chr6_31000001_34000001 chr6_32000001_35000001 chr8_8000001_11000001 chr8_9000001_12000001 chr11_47000001_50000001 chr11_48000001_51000001 chr11_49000001_52000001 chr11_50000001_53000001

--2023-12-08 16:27:00--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr11_47000001_50000001.gz
Resolving broad-alkesgroup-ukbb-ld.s3.amazonaws.com (broad-alkesgroup-ukbb-ld.s3.amazonaws.com)... 54.231.132.9, 16.182.74.217, 3.5.20.10, ...
Connecting to broad-alkesgroup-ukbb-ld.s3.amazonaws.com (broad-alkesgroup-ukbb-ld.s3.amazonaws.com)|54.231.132.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 205659 (201K) [binary/octet-stream]
Saving to: ‘chr11_47000001_50000001.gz.1’

100%[========================================================================================================================>] 205,659     --.-K/s   in 0.09s   

2023-12-08 16:27:00 (2.14 MB/s) - ‘chr11_47000001_50000001.gz.1’ saved [205659/205659]

--2023-12-08 16:27:00--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr11_47000001_50000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:00 ERROR 404: Not Found.

--2023-12-08 16:27:00--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr11_48000001_51000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 221785 (217K) [binary/octet-stream]
Saving to: ‘chr11_48000001_51000001.gz.1’

100%[========================================================================================================================>] 221,785     --.-K/s   in 0.03s   

2023-12-08 16:27:00 (7.03 MB/s) - ‘chr11_48000001_51000001.gz.1’ saved [221785/221785]

--2023-12-08 16:27:00--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr11_48000001_51000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:01 ERROR 404: Not Found.

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr11_49000001_52000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 184853 (181K) [binary/octet-stream]
Saving to: ‘chr11_49000001_52000001.gz.1’

100%[========================================================================================================================>] 184,853     --.-K/s   in 0.01s   

2023-12-08 16:27:01 (12.8 MB/s) - ‘chr11_49000001_52000001.gz.1’ saved [184853/184853]

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr11_49000001_52000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:01 ERROR 404: Not Found.

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr11_50000001_53000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 121584 (119K) [binary/octet-stream]
Saving to: ‘chr11_50000001_53000001.gz.1’

100%[========================================================================================================================>] 121,584     --.-K/s   in 0.001s  

2023-12-08 16:27:01 (141 MB/s) - ‘chr11_50000001_53000001.gz.1’ saved [121584/121584]

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr11_50000001_53000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:01 ERROR 404: Not Found.

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr6_26000001_29000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 188489 (184K) [binary/octet-stream]
Saving to: ‘chr6_26000001_29000001.gz.1’

100%[========================================================================================================================>] 188,489     --.-K/s   in 0.004s  

2023-12-08 16:27:01 (51.1 MB/s) - ‘chr6_26000001_29000001.gz.1’ saved [188489/188489]

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr6_26000001_29000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:01 ERROR 404: Not Found.

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr6_27000001_30000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 252354 (246K) [binary/octet-stream]
Saving to: ‘chr6_27000001_30000001.gz.1’

100%[========================================================================================================================>] 252,354     --.-K/s   in 0.006s  

2023-12-08 16:27:01 (40.9 MB/s) - ‘chr6_27000001_30000001.gz.1’ saved [252354/252354]

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr6_27000001_30000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:01 ERROR 404: Not Found.

--2023-12-08 16:27:01--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr6_31000001_34000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 437289 (427K) [binary/octet-stream]
Saving to: ‘chr6_31000001_34000001.gz.1’

100%[========================================================================================================================>] 437,289     --.-K/s   in 0.03s   

2023-12-08 16:27:02 (13.3 MB/s) - ‘chr6_31000001_34000001.gz.1’ saved [437289/437289]

--2023-12-08 16:27:02--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr6_31000001_34000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:02 ERROR 404: Not Found.

--2023-12-08 16:27:02--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr6_32000001_35000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 368786 (360K) [binary/octet-stream]
Saving to: ‘chr6_32000001_35000001.gz.1’

100%[========================================================================================================================>] 368,786     --.-K/s   in 0.03s   

2023-12-08 16:27:02 (11.3 MB/s) - ‘chr6_32000001_35000001.gz.1’ saved [368786/368786]

--2023-12-08 16:27:02--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr6_32000001_35000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:02 ERROR 404: Not Found.

--2023-12-08 16:27:02--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr8_8000001_11000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 258058 (252K) [binary/octet-stream]
Saving to: ‘chr8_8000001_11000001.gz.1’

100%[========================================================================================================================>] 258,058     --.-K/s   in 0.007s  

2023-12-08 16:27:02 (34.6 MB/s) - ‘chr8_8000001_11000001.gz.1’ saved [258058/258058]

--2023-12-08 16:27:02--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr8_8000001_11000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:02 ERROR 404: Not Found.

--2023-12-08 16:27:02--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr8_9000001_12000001.gz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 261771 (256K) [binary/octet-stream]
Saving to: ‘chr8_9000001_12000001.gz.1’

100%[========================================================================================================================>] 261,771     --.-K/s   in 0.02s   

2023-12-08 16:27:02 (16.1 MB/s) - ‘chr8_9000001_12000001.gz.1’ saved [261771/261771]

--2023-12-08 16:27:02--  https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr8_9000001_12000001.npz
Reusing existing connection to broad-alkesgroup-ukbb-ld.s3.amazonaws.com:443.
HTTP request sent, awaiting response... 404 Not Found
2023-12-08 16:27:02 ERROR 404: Not Found.
omerwe commented 8 months ago

Please see the question about missing files in the FAQ