set environment
Code
source ../run_config_project.shshow_env
You are working on Duke Server: HARDAC
BASE DIRECTORY (FD_BASE): /data/reddylab/Kuei
REPO DIRECTORY (FD_REPO): /data/reddylab/Kuei/repo
WORK DIRECTORY (FD_WORK): /data/reddylab/Kuei/work
DATA DIRECTORY (FD_DATA): /data/reddylab/Kuei/data
CONTAINER DIR. (FD_SING): /data/reddylab/Kuei/container
You are working with ENCODE FCC
PATH OF PROJECT (FD_PRJ): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC
PROJECT RESULTS (FD_RES): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/results
PROJECT SCRIPTS (FD_EXE): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/scripts
PROJECT DATA (FD_DAT): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data
PROJECT NOTE (FD_NBK): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/notebooks
PROJECT DOCS (FD_DOC): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/docs
PROJECT LOG (FD_LOG): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/log
PROJECT APP (FD_APP): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/app
PROJECT REF (FD_REF): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/references
PROJECT IMAGE (FP_PRJ_SIF): /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/app/singularity_proj_encode_fcc.sif
Run the download script
Run the script that was generated in the previous step
Execute
Code
FD_OUT = ${FD_DAT} /external/encode_open_chromatincd ${FD_OUT} chmod +x ./run_download.sh./run_download.sh
Review
Check output files
Code
ls ${FD_OUT} /* .bed.gz | wc -l ls ${FD_OUT} /* .bed.gz | xargs -n 1 basename
6
K562.hg38.ENCSR000EKS.ENCFF274YGF.DNase.bed.gz
K562.hg38.ENCSR000EOT.ENCFF185XRG.DNase.bed.gz
K562.hg38.ENCSR483RKN.ENCFF558BLC.ATAC.bed.gz
K562.hg38.ENCSR483RKN.ENCFF925CYR.ATAC.bed.gz
K562.hg38.ENCSR868FGK.ENCFF333TAT.ATAC.bed.gz
K562.hg38.ENCSR868FGK.ENCFF948AFM.ATAC.bed.gz
Code
ls -lh ${FD_OUT} /* .bed.gz
-rw-rw-r-- 1 kk319 reddylab 1.3M Nov 24 2020 /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/encode_open_chromatin/K562.hg38.ENCSR000EKS.ENCFF274YGF.DNase.bed.gz
-rw-rw-r-- 1 kk319 reddylab 1.8M Nov 20 2020 /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/encode_open_chromatin/K562.hg38.ENCSR000EOT.ENCFF185XRG.DNase.bed.gz
-rw-rw-r-- 1 kk319 reddylab 4.8M Mar 2 2021 /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/encode_open_chromatin/K562.hg38.ENCSR483RKN.ENCFF558BLC.ATAC.bed.gz
-rw-rw-r-- 1 kk319 reddylab 2.7M Mar 2 2021 /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/encode_open_chromatin/K562.hg38.ENCSR483RKN.ENCFF925CYR.ATAC.bed.gz
-rw-rw-r-- 1 kk319 reddylab 6.8M Mar 19 2021 /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/encode_open_chromatin/K562.hg38.ENCSR868FGK.ENCFF333TAT.ATAC.bed.gz
-rw-rw-r-- 1 kk319 reddylab 4.1M Mar 19 2021 /data/reddylab/Kuei/repo/Proj_ENCODE_FCC/data/external/encode_open_chromatin/K562.hg38.ENCSR868FGK.ENCFF948AFM.ATAC.bed.gz
Check execution log
Code
head -n 10 ${FD_OUT} /run_download.log.txt
--2024-04-29 14:42:28-- https://www.encodeproject.org/files/ENCFF357GNC/@@download/ENCFF357GNC.bigWig
Resolving www.encodeproject.org (www.encodeproject.org)... 34.211.244.144
Connecting to www.encodeproject.org (www.encodeproject.org)|34.211.244.144|:443... connected.
HTTP request sent, awaiting response... 307 Temporary Redirect
Location: https://encode-public.s3.amazonaws.com/2021/03/16/9ff8b5ae-10d6-4711-96ea-a3cbb44aaadb/ENCFF357GNC.bigWig?response-content-disposition=attachment%3B%20filename%3DENCFF357GNC.bigWig&AWSAccessKeyId=ASIATGZNGCNXZJNTIWVL&Signature=ZCH2OcwIvhMklR26IbdBHzNlrlc%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEMP%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIHfDoL%2FkyNuJSfE5e58XEMDFZL2ZrtcD43gS5SNwI%2FGSAiEAgSPEY8cYGjol9F6QCo0Rq21KNvLUEqipUEhKdg57hGIqswUIHBAAGgwyMjA3NDg3MTQ4NjMiDP%2FLRjV5%2BOB5Hl3DLSqQBRtgZo1MbccqvpJe0xY4AGcq34zs1w60Icvmy8xRACyuPIeBkBfr9f15LH3cRIJmftU0%2B29HnHnAUp%2B%2BhU7z4LmGmqN0AHSKpPythUmjxdaWQRuPVNS8dfofAZhu5ItTakjczM8IusAup1jjYRCBOOPK74X8uwAvXfndiz5ETO6fcxcG2TIaFDoRPWjX%2FW6jmjbS3NUK%2BlheUToUTLKqiC9tyVHSb0J5zFrU6Dcdgjua9h8dPyQfKOy4iTVltlrV3qPSCatSOmZcw4Km49vV0eOk%2FP7b6qNx027sJ3Rx7zZ9lOKLzG7Xq7TTflVlF1HmzYs3FZHtT8sgxR8Twaf8Tckafar9hTpaI6s3334FxSZwUPta2iQdEEMl1Pta10NElCuoHhUlA0QtEXBWZpZW%2BKjwqMvY5wOQq%2BaFlYM%2BXWVMMl%2FDY6Kky1VHfCgbM0aVIsdQIDKUsSczQX11bxr8%2BP4XSC38QXuRLAeMRFhvTOQLixCf00ywlYiZYqSppIEI5yzl1ZnkuMgo4Vy%2Bk6cXWNX0EungZleFRTSzaMhxtfJWSJOzhH0o44K6pV6xaFykbtgX3m6oJhf%2FyCkaLnWqdYwsrIbhky66OJED2%2F67I4959ToX3jem5Ji6u0Sebe2gvVU6XFSwwSa255EwBx6GegSDo74O10AKWGOToZXwqHRUlEaY3DS2fOgT4zT9QbF4d0vinpAhKUSCgpcs2t4coZRQdjmlbRLUXVQjmKqEOJPIT%2FiQFj2xvHHn2a4Cv%2BQBjLUfyebupDmeX3CsHDiB74RqMX8TYGYm4SztYNoHgZsEeQ3EAjgQFRNBH1%2FwcbrOGxIPSvI9z0ayj9F46a2r2XXyjAlTwj4aAo8K77IF8HDdMKHNv7EGOrEBbRlsSibEbVGS7a2bdYrlWpHv0pld%2B3AxRSf%2FYBl6fZ4dWfzQnlTH6wir5%2FkcVX4H6%2FKbxHjb7wAztGEOIgqC%2B2vl%2Fle4CjtsW4wuHODHYaIuaaHMjkVA1wCIW2qZ%2B8bt67q%2F41RwvXLWSzBcSkFt5l70x6Z7E1uZxSdr4xGLNVLLuvY%2FHsQj2bgCy8GSEQ57InO48TfSy3T6G7gDIZpoTO93m%2FSMvNTzUi2hgPC1zy4c&Expires=1714545748 [following]
--2024-04-29 14:42:28-- https://encode-public.s3.amazonaws.com/2021/03/16/9ff8b5ae-10d6-4711-96ea-a3cbb44aaadb/ENCFF357GNC.bigWig?response-content-disposition=attachment%3B%20filename%3DENCFF357GNC.bigWig&AWSAccessKeyId=ASIATGZNGCNXZJNTIWVL&Signature=ZCH2OcwIvhMklR26IbdBHzNlrlc%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEMP%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJHMEUCIHfDoL%2FkyNuJSfE5e58XEMDFZL2ZrtcD43gS5SNwI%2FGSAiEAgSPEY8cYGjol9F6QCo0Rq21KNvLUEqipUEhKdg57hGIqswUIHBAAGgwyMjA3NDg3MTQ4NjMiDP%2FLRjV5%2BOB5Hl3DLSqQBRtgZo1MbccqvpJe0xY4AGcq34zs1w60Icvmy8xRACyuPIeBkBfr9f15LH3cRIJmftU0%2B29HnHnAUp%2B%2BhU7z4LmGmqN0AHSKpPythUmjxdaWQRuPVNS8dfofAZhu5ItTakjczM8IusAup1jjYRCBOOPK74X8uwAvXfndiz5ETO6fcxcG2TIaFDoRPWjX%2FW6jmjbS3NUK%2BlheUToUTLKqiC9tyVHSb0J5zFrU6Dcdgjua9h8dPyQfKOy4iTVltlrV3qPSCatSOmZcw4Km49vV0eOk%2FP7b6qNx027sJ3Rx7zZ9lOKLzG7Xq7TTflVlF1HmzYs3FZHtT8sgxR8Twaf8Tckafar9hTpaI6s3334FxSZwUPta2iQdEEMl1Pta10NElCuoHhUlA0QtEXBWZpZW%2BKjwqMvY5wOQq%2BaFlYM%2BXWVMMl%2FDY6Kky1VHfCgbM0aVIsdQIDKUsSczQX11bxr8%2BP4XSC38QXuRLAeMRFhvTOQLixCf00ywlYiZYqSppIEI5yzl1ZnkuMgo4Vy%2Bk6cXWNX0EungZleFRTSzaMhxtfJWSJOzhH0o44K6pV6xaFykbtgX3m6oJhf%2FyCkaLnWqdYwsrIbhky66OJED2%2F67I4959ToX3jem5Ji6u0Sebe2gvVU6XFSwwSa255EwBx6GegSDo74O10AKWGOToZXwqHRUlEaY3DS2fOgT4zT9QbF4d0vinpAhKUSCgpcs2t4coZRQdjmlbRLUXVQjmKqEOJPIT%2FiQFj2xvHHn2a4Cv%2BQBjLUfyebupDmeX3CsHDiB74RqMX8TYGYm4SztYNoHgZsEeQ3EAjgQFRNBH1%2FwcbrOGxIPSvI9z0ayj9F46a2r2XXyjAlTwj4aAo8K77IF8HDdMKHNv7EGOrEBbRlsSibEbVGS7a2bdYrlWpHv0pld%2B3AxRSf%2FYBl6fZ4dWfzQnlTH6wir5%2FkcVX4H6%2FKbxHjb7wAztGEOIgqC%2B2vl%2Fle4CjtsW4wuHODHYaIuaaHMjkVA1wCIW2qZ%2B8bt67q%2F41RwvXLWSzBcSkFt5l70x6Z7E1uZxSdr4xGLNVLLuvY%2FHsQj2bgCy8GSEQ57InO48TfSy3T6G7gDIZpoTO93m%2FSMvNTzUi2hgPC1zy4c&Expires=1714545748
Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.92.227.73, 52.218.237.131, 52.92.205.57, ...
Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.92.227.73|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2118644361 (2.0G) [binary/octet-stream]