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
Code
TXT_FOLDER = hic_insitu_K562_ENCSR545YBD
Run the download script
Run the script that was generated in the previous step
Execute
Code
FD_OUT = ${FD_DAT} /external/${TXT_FOLDER} cd ${FD_OUT} chmod +x ./run_download.sh./run_download.sh
Review
Check output files
Code
ls ${FD_OUT} | xargs -n 1 basename
K562.hg38.ENCSR545YBD.ENCFF271SAF.hic_insitu.contact_domain.bedpe.gz
K562.hg38.ENCSR545YBD.ENCFF616PUW.hic_insitu.matrix.hic
K562.hg38.ENCSR545YBD.ENCFF693XIL.hic_insitu.loops.bedpe.gz
run_download.log.txt
run_download.sh
Code
total 22G
-rw-rw-r-- 1 kk319 reddylab 293K Jan 24 2023 K562.hg38.ENCSR545YBD.ENCFF271SAF.hic_insitu.contact_domain.bedpe.gz
-rw-rw-r-- 1 kk319 reddylab 22G Jan 24 2023 K562.hg38.ENCSR545YBD.ENCFF616PUW.hic_insitu.matrix.hic
-rw-rw-r-- 1 kk319 reddylab 880K Jan 24 2023 K562.hg38.ENCSR545YBD.ENCFF693XIL.hic_insitu.loops.bedpe.gz
-rw-rw-r-- 1 kk319 reddylab 34M May 2 15:46 run_download.log.txt
-rwxrwxr-x 1 kk319 reddylab 603 May 2 15:32 run_download.sh
Code
FP_OUT = ${FD_OUT} /K562.hg38.ENCSR545YBD.ENCFF693XIL.hic_insitu.loops.bedpe.gzzcat ${FP_OUT} | head -n 5
#chr1 x1 x2 chr2 y1 y2 name score strand1 strand2 color observed expectedBL expectedDonut expectedH expectedV fdrBL fdrDonut fdrH fdrV numCollapsed centroid1 centroid2 radius
# juicer_tools version 2.13.06
chr10 34010000 34020000 chr10 35050000 35060000 . . . . 0,255,255 25.0 6.6749783 6.117001 6.028173 4.855595 0.0036679406 3.0621103E-4 3.4923825E-4 6.161639E-6 1 34015000 35055000 0
chr10 124000000 124005000 chr10 124380000 124385000 . . . . 0,255,255 38.0 13.690522 14.195029 18.101181 18.336344 0.0022106771 0.0023932518 0.058508653 0.059743028 3 123997500 124387500 7071
chr10 133330000 133335000 chr10 133495000 133500000 . . . . 0,255,255 39.0 14.323421 15.468441 18.856985 18.800962 0.0011134844 0.0011820481 0.037496306 0.038466662 2 133330000 133500000 3536
Code
FP_OUT = ${FD_OUT} /K562.hg38.ENCSR545YBD.ENCFF271SAF.hic_insitu.contact_domain.bedpe.gzzcat ${FP_OUT} | head -n 5
#chr1 x1 x2 chr2 y1 y2 name score strand1 strand2 color score uVarScore lVarScore upSign loSign
# juicer_tools version 2.13.06
chr10 84565000 86085000 chr10 84565000 86085000 . . . . 255,255,0 0.797322669093712 0.36036680286901346 0.34029928924052977 0.44465944272445823 0.547858617131063
chr10 50985000 52225000 chr10 50985000 52225000 . . . . 255,255,0 1.0083018408826874 0.3171058429109649 0.34772601741376474 0.5433548387096774 0.4545161290322581
chr10 98415000 99300000 chr10 98415000 99300000 . . . . 255,255,0 0.6516994003966435 0.2746901933484111 0.28586117952993195 0.4402221941674031 0.6153263476833734
Check execution log
Code
head -n 10 ${FD_OUT} /run_download.log.txt
--2024-05-02 15:34:35-- https://www.encodeproject.org/files/ENCFF616PUW/@@download/ENCFF616PUW.hic
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/2022/10/10/0332f11a-aa2a-4532-9615-5b42b55ea5c3/ENCFF616PUW.hic?response-content-disposition=attachment%3B%20filename%3DENCFF616PUW.hic&AWSAccessKeyId=ASIATGZNGCNXR3L4ZKMY&Signature=faTvELv2J0DHQgbiE3t72r9jI2E%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEAsaCXVzLXdlc3QtMiJIMEYCIQDFn4xV49f4H2d%2BsUDx7CV4DLpzASOUFpb0ToTdr4dmcgIhAPgUjjG%2F81sRE%2BygD62Cpjd2AJGDQpqdu59K%2F1WwsEL2KrMFCGQQABoMMjIwNzQ4NzE0ODYzIgzuRYgAD%2BCPG4U7K3gqkAW3NuXXZB%2FcE5VngsuguJIdNdM%2Bm8bC4q5vmsDqbvBrxYd1sf9clmSoXjIPaY3cw1%2FqKSkHThMGEoGdOiA35kXR2N1pZ1ZmIdFULjMbH4vKTwRgDrIbyU%2BYX76bw5hUoPsKX9s6vwvlQXskTJZp7ktX2Fetd5Xemr1zO0vQV5loNL8nY9phweQJxuinCqAjEjS6XGDDDxZxiCWmsPhVCJeXLlQI%2FbCJtwtDimxeXet42qWnq5KMarBZ8A%2BX1QNws3A92E6fWS4keUdPWyrWbFPh21IoS8A%2BDvSCOkEARX4JxVqV6w91ZS2MFrj%2F3sMW7xAyFF%2BT%2B6x41VO%2Bz3JV2yrxTOS76qQ05XQrOcYnpfEmPavmSDc7hoo0DpLrXwSToybd0gqP24EklEneb3%2Bh0qDnlI96G8tWdCk%2B9dqpPgQlXoB0tH46S%2BtYVsYr2xQe0kPKpVDptu15RNwhddZ%2BM7jRFjMfB058cC0oZ8dbyckJc4gzFCFILQIt6vElrkkUJnu3I6JYXZg1zHG22khRZEHDqQNg2uA%2BfkScL2YnEECPb3gFNM4tdWnl6OYDJm85QFY9CRpdCLl%2F%2BXK3B7%2B4jKv1mk7Za3%2BJvMH84lXZhEc1ICQbN4JKUgjWMgOpWuQNO1uz%2BaUJHPnPbqDfXiFn4uQVPHV9N2BwpF2u58xbv30APeax0X0WBGMriBDlsxLmBMDVtqhA2NBynCmPHNG%2BBSfWuF3IPww6wLrh%2B3ce8zYjkfpn0g1o4RvDaCW2UXo2%2FhP4u5u8CQNVXYJ0BaWvovVSX4lvGpVxJT%2BUif5J%2Fue64Y%2FetkdINsOVk1XJtz0oIf038VJ4J58V6Tvw1gHbVtoic%2B4blZebW%2Ba5nhORLk26kjCWy8%2BxBjqwAV5rlnkaaUttgzPUZmBXtPCavUeUumz24ToeqAN68ioNUe04CFRA8UHOVPfvY3LgMmbaCklmvMntZuPay4rahvcyE4yYth19rvuKpKqPYySdAOaHYYfOzVCzrIH8Te84C6%2FeM7n8mBhkkzLLOVW2fo0aq4yqPG8nVAoaO%2F%2FdQ0%2Fs0WDQB%2FdUNZtJSEaT%2BHR2NRMHTa%2FJBnZqEpqMRH%2BHduJkVlI6skkS%2Bu%2BxCFiBczWg&Expires=1714808075 [following]
--2024-05-02 15:34:35-- https://encode-public.s3.amazonaws.com/2022/10/10/0332f11a-aa2a-4532-9615-5b42b55ea5c3/ENCFF616PUW.hic?response-content-disposition=attachment%3B%20filename%3DENCFF616PUW.hic&AWSAccessKeyId=ASIATGZNGCNXR3L4ZKMY&Signature=faTvELv2J0DHQgbiE3t72r9jI2E%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEAsaCXVzLXdlc3QtMiJIMEYCIQDFn4xV49f4H2d%2BsUDx7CV4DLpzASOUFpb0ToTdr4dmcgIhAPgUjjG%2F81sRE%2BygD62Cpjd2AJGDQpqdu59K%2F1WwsEL2KrMFCGQQABoMMjIwNzQ4NzE0ODYzIgzuRYgAD%2BCPG4U7K3gqkAW3NuXXZB%2FcE5VngsuguJIdNdM%2Bm8bC4q5vmsDqbvBrxYd1sf9clmSoXjIPaY3cw1%2FqKSkHThMGEoGdOiA35kXR2N1pZ1ZmIdFULjMbH4vKTwRgDrIbyU%2BYX76bw5hUoPsKX9s6vwvlQXskTJZp7ktX2Fetd5Xemr1zO0vQV5loNL8nY9phweQJxuinCqAjEjS6XGDDDxZxiCWmsPhVCJeXLlQI%2FbCJtwtDimxeXet42qWnq5KMarBZ8A%2BX1QNws3A92E6fWS4keUdPWyrWbFPh21IoS8A%2BDvSCOkEARX4JxVqV6w91ZS2MFrj%2F3sMW7xAyFF%2BT%2B6x41VO%2Bz3JV2yrxTOS76qQ05XQrOcYnpfEmPavmSDc7hoo0DpLrXwSToybd0gqP24EklEneb3%2Bh0qDnlI96G8tWdCk%2B9dqpPgQlXoB0tH46S%2BtYVsYr2xQe0kPKpVDptu15RNwhddZ%2BM7jRFjMfB058cC0oZ8dbyckJc4gzFCFILQIt6vElrkkUJnu3I6JYXZg1zHG22khRZEHDqQNg2uA%2BfkScL2YnEECPb3gFNM4tdWnl6OYDJm85QFY9CRpdCLl%2F%2BXK3B7%2B4jKv1mk7Za3%2BJvMH84lXZhEc1ICQbN4JKUgjWMgOpWuQNO1uz%2BaUJHPnPbqDfXiFn4uQVPHV9N2BwpF2u58xbv30APeax0X0WBGMriBDlsxLmBMDVtqhA2NBynCmPHNG%2BBSfWuF3IPww6wLrh%2B3ce8zYjkfpn0g1o4RvDaCW2UXo2%2FhP4u5u8CQNVXYJ0BaWvovVSX4lvGpVxJT%2BUif5J%2Fue64Y%2FetkdINsOVk1XJtz0oIf038VJ4J58V6Tvw1gHbVtoic%2B4blZebW%2Ba5nhORLk26kjCWy8%2BxBjqwAV5rlnkaaUttgzPUZmBXtPCavUeUumz24ToeqAN68ioNUe04CFRA8UHOVPfvY3LgMmbaCklmvMntZuPay4rahvcyE4yYth19rvuKpKqPYySdAOaHYYfOzVCzrIH8Te84C6%2FeM7n8mBhkkzLLOVW2fo0aq4yqPG8nVAoaO%2F%2FdQ0%2Fs0WDQB%2FdUNZtJSEaT%2BHR2NRMHTa%2FJBnZqEpqMRH%2BHduJkVlI6skkS%2Bu%2BxCFiBczWg&Expires=1714808075
Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.92.249.241, 52.92.241.145, 52.92.163.137, ...
Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.92.249.241|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 22638682080 (21G) [binary/octet-stream]