search

kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
159 stars 81 forks source link

trouble installing genome data for mm10 #142

Closed eunsolp closed 5 years ago

eunsolp commented 5 years ago

Hello,

I have trouble downloading genome data for mm10 as well as hg19. when I ran the command [bash install_genome_data.sh mm10 /home/eunsolp] I get this error message:

Downloading files... --2019-01-03 10:03:50-- https://www.encodeproject.org/files/mm10_no_alt_analysis_set_ENCODE/@@download/mm10_no_alt_analysis_set_ENCODE.fasta.gz Resolving www.encodeproject.org... 171.67.205.70 Connecting to www.encodeproject.org|171.67.205.70|:443... connected. HTTP request sent, awaiting response... 307 Temporary Redirect Location: https://download.encodeproject.org/https://encode-files.s3.amazonaws.com/2016/01/23/b6a24661-be65-48a4-9e4e-44a007f35f5c/mm10_no_alt_analysis_set_ENCODE.fasta.gz?response-content-disposition=attachment%3B%20filename%3Dmm10_no_alt_analysis_set_ENCODE.fasta.gz&Expires=1546657430&Signature=aCtJK21EF8MuJjCdYSHGRisBRzk%3D&x-amz-security-token=FQoGZXIvYXdzEKT%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaDN5AOjGxGG9o4g2j1CK3A%2B56BbiYTDH6keLy4%2BbC8KR9zF1pRjIj5Y0kYcSMm2%2FINaSUEKvhKwbJFwFuVS95H6lmQcRn%2BrMMxqJemME91RH9VmPjUnPS9%2Blk0g4eu0wiH7qBtyk1X0Xj%2FPoutz0MMB9EToL9tQVo3BKubV8yb3vZPB5ygIVG4kjqAjwTyCfgLs59HZDt3y0EocKzAGn6Wr69rfDNenAlT%2BM9doupXCEspwyCNTiLtVH6APp%2Bi0vhupEUTJqZm28jW%2BLXDUL9U3IC0XMeklpUojY4Yf9uzYJkxeTulm%2BB87dKEWomRIyJOKrKkYXDEPAfB6V9W%2FzMtopqlc%2BshjvfyetbQUCJqXuR7a8YUgFVgcS7GBC28RU2MnttzjgjSwodier8B%2B50c9Ml52mVDkyRovOmDFA%2FWTO9RdQjB0%2FN5%2BJ9Ij32E%2FYuCs7q2cQVqro4nkvK9vMNb0RSlW0w2Po1zjGg7rTfdl0XrwjCUHJvoOpbyIk61KzwgvdAP%2BB2EZnxS1SRXyB0Sv9Pthxzprex%2BR8i58R0SLNOKjVxPzlrBfFxvc9tSgfTzuNdxtDkhJX8yqkrraknaJpz3rP04qYo%2FNa34QU%3D&AWSAccessKeyId=ASIATGZNGCNXST2TGH4Q [following] --2019-01-03 10:03:50-- https://download.encodeproject.org/https://encode-files.s3.amazonaws.com/2016/01/23/b6a24661-be65-48a4-9e4e-44a007f35f5c/mm10_no_alt_analysis_set_ENCODE.fasta.gz?response-content-disposition=attachment%3B%20filename%3Dmm10_no_alt_analysis_set_ENCODE.fasta.gz&Expires=1546657430&Signature=aCtJK21EF8MuJjCdYSHGRisBRzk%3D&x-amz-security-token=FQoGZXIvYXdzEKT%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaDN5AOjGxGG9o4g2j1CK3A%2B56BbiYTDH6keLy4%2BbC8KR9zF1pRjIj5Y0kYcSMm2%2FINaSUEKvhKwbJFwFuVS95H6lmQcRn%2BrMMxqJemME91RH9VmPjUnPS9%2Blk0g4eu0wiH7qBtyk1X0Xj%2FPoutz0MMB9EToL9tQVo3BKubV8yb3vZPB5ygIVG4kjqAjwTyCfgLs59HZDt3y0EocKzAGn6Wr69rfDNenAlT%2BM9doupXCEspwyCNTiLtVH6APp%2Bi0vhupEUTJqZm28jW%2BLXDUL9U3IC0XMeklpUojY4Yf9uzYJkxeTulm%2BB87dKEWomRIyJOKrKkYXDEPAfB6V9W%2FzMtopqlc%2BshjvfyetbQUCJqXuR7a8YUgFVgcS7GBC28RU2MnttzjgjSwodier8B%2B50c9Ml52mVDkyRovOmDFA%2FWTO9RdQjB0%2FN5%2BJ9Ij32E%2FYuCs7q2cQVqro4nkvK9vMNb0RSlW0w2Po1zjGg7rTfdl0XrwjCUHJvoOpbyIk61KzwgvdAP%2BB2EZnxS1SRXyB0Sv9Pthxzprex%2BR8i58R0SLNOKjVxPzlrBfFxvc9tSgfTzuNdxtDkhJX8yqkrraknaJpz3rP04qYo%2FNa34QU%3D&AWSAccessKeyId=ASIATGZNGCNXST2TGH4Q Resolving download.encodeproject.org... 171.67.205.70 Connecting to download.encodeproject.org|171.67.205.70|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://encode-files.s3.amazonaws.com/2016/01/23/b6a24661-be65-48a4-9e4e-44a007f35f5c/mm10_no_alt_analysis_set_ENCODE.fasta.gz?response-content-disposition=attachment%3B%20filename%3Dmm10_no_alt_analysis_set_ENCODE.fasta.gz&Expires=1546657430&Signature=aCtJK21EF8MuJjCdYSHGRisBRzk%3D&x-amz-security-token=FQoGZXIvYXdzEKT%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaDN5AOjGxGG9o4g2j1CK3A%2B56BbiYTDH6keLy4%2BbC8KR9zF1pRjIj5Y0kYcSMm2%2FINaSUEKvhKwbJFwFuVS95H6lmQcRn%2BrMMxqJemME91RH9VmPjUnPS9%2Blk0g4eu0wiH7qBtyk1X0Xj%2FPoutz0MMB9EToL9tQVo3BKubV8yb3vZPB5ygIVG4kjqAjwTyCfgLs59HZDt3y0EocKzAGn6Wr69rfDNenAlT%2BM9doupXCEspwyCNTiLtVH6APp%2Bi0vhupEUTJqZm28jW%2BLXDUL9U3IC0XMeklpUojY4Yf9uzYJkxeTulm%2BB87dKEWomRIyJOKrKkYXDEPAfB6V9W%2FzMtopqlc%2BshjvfyetbQUCJqXuR7a8YUgFVgcS7GBC28RU2MnttzjgjSwodier8B%2B50c9Ml52mVDkyRovOmDFA%2FWTO9RdQjB0%2FN5%2BJ9Ij32E%2FYuCs7q2cQVqro4nkvK9vMNb0RSlW0w2Po1zjGg7rTfdl0XrwjCUHJvoOpbyIk61KzwgvdAP%2BB2EZnxS1SRXyB0Sv9Pthxzprex%2BR8i58R0SLNOKjVxPzlrBfFxvc9tSgfTzuNdxtDkhJX8yqkrraknaJpz3rP04qYo%2FNa34QU%3D&AWSAccessKeyId=ASIATGZNGCNXST2TGH4Q [following] --2019-01-03 10:03:50-- https://encode-files.s3.amazonaws.com/2016/01/23/b6a24661-be65-48a4-9e4e-44a007f35f5c/mm10_no_alt_analysis_set_ENCODE.fasta.gz?response-content-disposition=attachment%3B%20filename%3Dmm10_no_alt_analysis_set_ENCODE.fasta.gz&Expires=1546657430&Signature=aCtJK21EF8MuJjCdYSHGRisBRzk%3D&x-amz-security-token=FQoGZXIvYXdzEKT%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaDN5AOjGxGG9o4g2j1CK3A%2B56BbiYTDH6keLy4%2BbC8KR9zF1pRjIj5Y0kYcSMm2%2FINaSUEKvhKwbJFwFuVS95H6lmQcRn%2BrMMxqJemME91RH9VmPjUnPS9%2Blk0g4eu0wiH7qBtyk1X0Xj%2FPoutz0MMB9EToL9tQVo3BKubV8yb3vZPB5ygIVG4kjqAjwTyCfgLs59HZDt3y0EocKzAGn6Wr69rfDNenAlT%2BM9doupXCEspwyCNTiLtVH6APp%2Bi0vhupEUTJqZm28jW%2BLXDUL9U3IC0XMeklpUojY4Yf9uzYJkxeTulm%2BB87dKEWomRIyJOKrKkYXDEPAfB6V9W%2FzMtopqlc%2BshjvfyetbQUCJqXuR7a8YUgFVgcS7GBC28RU2MnttzjgjSwodier8B%2B50c9Ml52mVDkyRovOmDFA%2FWTO9RdQjB0%2FN5%2BJ9Ij32E%2FYuCs7q2cQVqro4nkvK9vMNb0RSlW0w2Po1zjGg7rTfdl0XrwjCUHJvoOpbyIk61KzwgvdAP%2BB2EZnxS1SRXyB0Sv9Pthxzprex%2BR8i58R0SLNOKjVxPzlrBfFxvc9tSgfTzuNdxtDkhJX8yqkrraknaJpz3rP04qYo%2FNa34QU%3D&AWSAccessKeyId=ASIATGZNGCNXST2TGH4Q Resolving encode-files.s3.amazonaws.com... 52.218.248.138 Connecting to encode-files.s3.amazonaws.com|52.218.248.138|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 870379095 (830M) [binary/octet-stream] Saving to: "mm10_no_alt_analysis_set_ENCODE.fasta.gz"

100%[===============================================================>] 870,379,095 20.8M/s in 41s

2019-01-03 10:04:32 (20.3 MB/s) - "mm10_no_alt_analysis_set_ENCODE.fasta.gz" saved [870379095/870379095]

--2019-01-03 10:04:32-- http://mitra.stanford.edu/kundaje/genome_data/mm10/mm10.blacklist.bed.gz Resolving mitra.stanford.edu... 171.67.96.243 Connecting to mitra.stanford.edu|171.67.96.243|:80... connected. HTTP request sent, awaiting response... 404 Not Found 2019-01-03 10:04:32 ERROR 404: Not Found.

It seems like some of mm10 data has been removed from the server. Could you help me with this?

Thank you, Eunsol

leepc12 commented 5 years ago

Please update your pipeline (git pull) and try again.

eunsolp commented 5 years ago

I ran git pull and it says it is already up to date. I re installed mm10 genome data and it still gives me the same error.

leepc12 commented 5 years ago

Fixed. Please git pull and try again.

BTW this pipeline has been deprecated and no longer maintained. Please try a new one at https://github.com/encode-dcc/atac-seq-pipeline.

eunsolp commented 5 years ago

Alright, thank you!