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_intact_K562_ENCSR479XDG
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.ENCSR479XDG.ENCFF126GED.hic_intact.contact_domain.bedpe.gz
K562.hg38.ENCSR479XDG.ENCFF256ZMD.hic_intact.loops.bedpe.gz
K562.hg38.ENCSR479XDG.ENCFF621AIY.hic_intact.matrix.hic
run_download.log.txt
run_download.sh
Code
total 32G
-rw-rw-r-- 1 kk319 reddylab 219K Nov 13 2022 K562.hg38.ENCSR479XDG.ENCFF126GED.hic_intact.contact_domain.bedpe.gz
-rw-rw-r-- 1 kk319 reddylab 2.8M Nov 13 2022 K562.hg38.ENCSR479XDG.ENCFF256ZMD.hic_intact.loops.bedpe.gz
-rw-rw-r-- 1 kk319 reddylab 32G Nov 10 2022 K562.hg38.ENCSR479XDG.ENCFF621AIY.hic_intact.matrix.hic
-rw-rw-r-- 1 kk319 reddylab 51M May 2 17:45 run_download.log.txt
-rwxrwxr-x 1 kk319 reddylab 603 May 2 17:27 run_download.sh
Code
FP_OUT = ${FD_OUT} /K562.hg38.ENCSR479XDG.ENCFF256ZMD.hic_intact.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 highRes_start_1 highRes_end_1 highRes_start_2 highRes_end_2 localX localY localObserved localPval localPeakID
# juicer_tools version 2.13.07
chr10 102835000 102836000 chr10 102901000 102902000 . . . . 0,255,255 16.0 2.5453029 2.0566912 2.896359 2.6027875 0.0 0.0 5.9604645E-8 0.0 2 102835000 102901500 500 102834600 102835200 102901400 102901700 102834700 102901500 4.0 2.17173181723318E-4 0
chr10 123583000 123584000 chr10 123967000 123968000 . . . . 0,255,255 17.0 1.2294405 1.126373 1.5320965 2.968846 0.0 0.0 0.0 0.0 2 123583000 123967500 500 NA NA NA NA NA NA NA NA NA
chr10 60780000 60782000 chr10 60828000 60830000 . . . . 0,255,255 16.0 3.9354546 3.6036625 4.087633 2.7198699 3.993511E-6 1.3113022E-6 6.377697E-6 5.9604645E-8 1 60781000 60829000 0 NA NA NA NA NA NA NA NA NA
Code
FP_OUT = ${FD_OUT} /K562.hg38.ENCSR479XDG.ENCFF126GED.hic_intact.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 89790000 90730000 chr10 89790000 90730000 . . . . 255,255,0 0.48733428805910184 0.43218752937273686 0.39101424267719964 0.4366181410974244 0.5132138857782754
chr10 117485000 118260000 chr10 117485000 118260000 . . . . 255,255,0 0.47145995448002187 0.40388060738386966 0.40280872469677464 0.44690992767915844 0.4451019066403682
chr10 51125000 52215000 chr10 51125000 52215000 . . . . 255,255,0 0.575707559391474 0.38559880334456653 0.3954850048221743 0.47122602168473726 0.40008340283569643
Check execution log
Code
head -n 10 ${FD_OUT} /run_download.log.txt
--2024-05-02 17:27:59-- https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.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/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic?response-content-disposition=attachment%3B%20filename%3DENCFF621AIY.hic&AWSAccessKeyId=ASIATGZNGCNXWCWCL4OE&Signature=3NvvPpiax3yeE7%2FE4wWH5CuDsSQ%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEA4aCXVzLXdlc3QtMiJGMEQCIBpPJDCDpCVE1M1vw%2FGls2BE%2BFDxQ8WFkP9EWSCkOqZlAiBr7OX9Lb4BuCeL2Rzr2VonmZTiZLTREFMrvdXxSr9pDiqzBQhmEAAaDDIyMDc0ODcxNDg2MyIMP%2BrJcOeQq0JafnWlKpAFa5f7%2BX5lEZqVdYhDBt4%2BQmSGhQM%2BgTu8OBtUQy4fxsxQoTXpQDoEuqCjA7q1YtE5kSsb2lgURelfleGCt6j7YkGpYEqdFdh1auYeOaQKX99wGw2Yl3iLxn5WoBlUtbior0Pv4iGZtiNtMbiNmlvPQ5ahn654t42LjUZacPOo7XqXfHUjFEpd3uT3TSW68qg8reylYFMIRPr%2BRX6yMe64cImfiyFwOhbqK%2FlqQZ1qKHvC8mO3K9YAIceWtICkdbSMBs9gx1wMVyEnhSH70YvWvqsEqE6lx745%2F5VF%2FpujjxSLqegZj3m1jA94SMQi0DOSjRuOzXB%2FeUqaRECZQaxowHsn%2B02oAic16iIPyhMSDccLHfNRBDKa7WslPNfVsg25LlOQPQUfScCm4aq30AKjrczwM6tS7bLOCqc1fnLEE2GbMmrInXMeqCImMcb9NtYpbgsGFOq2922RBmJigTKexalmSQiNqsdqKIV7zN0qsAirdbvYiYyEQcwmApPcJ34mvrV2%2BaBLIqmt2lhUpOYiAtmEwCHt3J%2B8gh%2FVBOW9BOZmXGB3YKP8iml%2BUZKU2rj7F2KD9FhTu9zYh4sqf%2B4P7lLzKPkphab9pFalxiAkQyEdM1mzf6NkwE4xOMLHctJwLt9zsbpZE3EVrljDYU543IP2CdmZkY%2Fc6V18MrhUjLQOf3JxJvARjebkgkeGSRtmM%2BcvUqMuAvf7xLTdJOCPssaEwSFHUnSOhHDLWYeFkeMrxY2cRyiNxdnSStzTCW8a10%2FHt7t6hLMufKmW0fQ5o40E4LQ21uJY%2FSHl4CnBi1gS%2BK6XAC9sBT20KvNrRj%2BiJ7%2FIIXvjMWrs5ayUzowirGyFBzdsGiaDmE%2FzPfuV7aowuIfQsQY6sgEGZKLIo2jznU836Bwg3N8jv5Z%2BGaogkHJzbLTTGJXb%2F47XekGCYLL%2B3U9vry7tzpCyr1KpwHeD4mzxb7IL0%2B8uFIknYXwHsOYn7uM5%2Fo5NiTgKIxrFUAHTmcMtCxaf6CYoCbkljK%2FryI1kEDU3HR6Au%2F3tQg0Y1Eh2wYbQVNkH9nHLByXatcmz%2F%2B%2FU3zmahD%2By63A15Kw1GrRc8ykF2Y9eLvJLxHYMag0SrLIQkYNNSBv%2F&Expires=1714814879 [following]
--2024-05-02 17:27:59-- https://encode-public.s3.amazonaws.com/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic?response-content-disposition=attachment%3B%20filename%3DENCFF621AIY.hic&AWSAccessKeyId=ASIATGZNGCNXWCWCL4OE&Signature=3NvvPpiax3yeE7%2FE4wWH5CuDsSQ%3D&x-amz-security-token=IQoJb3JpZ2luX2VjEA4aCXVzLXdlc3QtMiJGMEQCIBpPJDCDpCVE1M1vw%2FGls2BE%2BFDxQ8WFkP9EWSCkOqZlAiBr7OX9Lb4BuCeL2Rzr2VonmZTiZLTREFMrvdXxSr9pDiqzBQhmEAAaDDIyMDc0ODcxNDg2MyIMP%2BrJcOeQq0JafnWlKpAFa5f7%2BX5lEZqVdYhDBt4%2BQmSGhQM%2BgTu8OBtUQy4fxsxQoTXpQDoEuqCjA7q1YtE5kSsb2lgURelfleGCt6j7YkGpYEqdFdh1auYeOaQKX99wGw2Yl3iLxn5WoBlUtbior0Pv4iGZtiNtMbiNmlvPQ5ahn654t42LjUZacPOo7XqXfHUjFEpd3uT3TSW68qg8reylYFMIRPr%2BRX6yMe64cImfiyFwOhbqK%2FlqQZ1qKHvC8mO3K9YAIceWtICkdbSMBs9gx1wMVyEnhSH70YvWvqsEqE6lx745%2F5VF%2FpujjxSLqegZj3m1jA94SMQi0DOSjRuOzXB%2FeUqaRECZQaxowHsn%2B02oAic16iIPyhMSDccLHfNRBDKa7WslPNfVsg25LlOQPQUfScCm4aq30AKjrczwM6tS7bLOCqc1fnLEE2GbMmrInXMeqCImMcb9NtYpbgsGFOq2922RBmJigTKexalmSQiNqsdqKIV7zN0qsAirdbvYiYyEQcwmApPcJ34mvrV2%2BaBLIqmt2lhUpOYiAtmEwCHt3J%2B8gh%2FVBOW9BOZmXGB3YKP8iml%2BUZKU2rj7F2KD9FhTu9zYh4sqf%2B4P7lLzKPkphab9pFalxiAkQyEdM1mzf6NkwE4xOMLHctJwLt9zsbpZE3EVrljDYU543IP2CdmZkY%2Fc6V18MrhUjLQOf3JxJvARjebkgkeGSRtmM%2BcvUqMuAvf7xLTdJOCPssaEwSFHUnSOhHDLWYeFkeMrxY2cRyiNxdnSStzTCW8a10%2FHt7t6hLMufKmW0fQ5o40E4LQ21uJY%2FSHl4CnBi1gS%2BK6XAC9sBT20KvNrRj%2BiJ7%2FIIXvjMWrs5ayUzowirGyFBzdsGiaDmE%2FzPfuV7aowuIfQsQY6sgEGZKLIo2jznU836Bwg3N8jv5Z%2BGaogkHJzbLTTGJXb%2F47XekGCYLL%2B3U9vry7tzpCyr1KpwHeD4mzxb7IL0%2B8uFIknYXwHsOYn7uM5%2Fo5NiTgKIxrFUAHTmcMtCxaf6CYoCbkljK%2FryI1kEDU3HR6Au%2F3tQg0Y1Eh2wYbQVNkH9nHLByXatcmz%2F%2B%2FU3zmahD%2By63A15Kw1GrRc8ykF2Y9eLvJLxHYMag0SrLIQkYNNSBv%2F&Expires=1714814879
Resolving encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)... 52.92.208.249, 52.92.225.193, 52.92.241.41, ...
Connecting to encode-public.s3.amazonaws.com (encode-public.s3.amazonaws.com)|52.92.208.249|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 33783625697 (31G) [binary/octet-stream]