Squashed commit of the following:

commit ea85956
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 24 16:31:02 2022 -0400

    trivial changes

commit 89b12b1
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 24 16:29:17 2022 -0400

    re-enable best model

commit 3623424
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 24 16:23:35 2022 -0400

    updated collate docker

commit 6ccc068
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 10 22:55:17 2022 -0400

    updated dgv_bed

commit 8761389
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 10 16:28:58 2022 -0400

    added subtraction of dgv

commit 24d8345
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 10 15:02:04 2022 -0400

    updated docker for create_tar_gz

commit e625499
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 10 14:41:53 2022 -0400

    updated dockers with new conda; updated .travis.yaml with new quay.io encrypted creds

commit 02f66e2
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 10 13:49:11 2022 -0400

    update miniconda to 4.11.0

commit 85996a7
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 10 13:43:10 2022 -0400

    re-enable empirical neutral regions

commit 44730bc
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 10 13:42:09 2022 -0400

    changed quay repo to ilya_broad_cms_ci

commit 2c5b8bd
Author: Ilya Shlyakhter <[email protected]>
Date:   Wed May 4 15:20:51 2022 -0400

    rerun best model

commit b1479cf
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 3 19:04:20 2022 -0400

    merge bioconda-recipes from master

commit 9bdc06d
Author: Ilya Shlyakhter <[email protected]>
Date:   Tue May 3 16:47:21 2022 -0400

    rename best model file to best_

commit 6aa98c2
Author: Ilya Shlyakhter <[email protected]>
Date:   Wed Apr 27 16:58:51 2022 -0400

    added ucsc-bigbedtobed to commontools

commit 267016d
Author: Ilya Shlyakhter <[email protected]>
Date:   Wed Apr 27 16:27:38 2022 -0400

    restore nre config

commit 2ef328a
Author: Ilya Shlyakhter <[email protected]>
Date:   Wed Apr 27 16:24:39 2022 -0400

    best model training data

commit acff954
Author: Ilya Shlyakhter <[email protected]>
Date:   Wed Apr 13 16:51:51 2022 -0400

    force nre rerun

commit 0a18cc3
Author: Ilya Shlyakhter <[email protected]>
Date:   Wed Apr 13 16:37:26 2022 -0400

    nre: enable empirical neutral regions workflow

.gitmodules

@@ -21,7 +21,8 @@
 	#url = ../cms2-work.git
 	url = ./
 	#branch = submodule--cms2-docker-component-stats--master
-	branch = is-211017-1453-restore-selscan-build
+	#branch = is-211017-1453-restore-selscan-build
+	branch = is-is-220510-1347-update-miniconda
 	shallow = true
 	fetchRecurseSubmodules = true
 

.travis.yml

@@ -18,7 +18,10 @@ env:
     # GH_TOKEN
     - secure: "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"
     # QUAY_CMS_TOKEN
-    - secure: "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"
+    - secure: "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"
+    # QUAY_ROBOT_TOKEN
+    - secure: "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"
+
 branches:
   except:
     - /.*-staging$/

README.org

@@ -55,4 +55,3 @@ Workflows to run population genetics simulations and compute component scores fo
 *** Neutral regions
 
     http://nre.cb.bscb.cornell.edu/nre/run.html Neutral Region Explorer
-

best_default_112115_825am__demography.par

@@ -0,0 +1,94 @@
+length 3000000
+mutation_rate 1.25e-08
+recomb_file /idi/sabeti-scratch/jvitti/params/test_recom.recom
+#/Users/vitti/Desktop/cms_ml_2/params/test_recom.recom
+gene_conversion_relative_rate 2.3
+
+pop_define 1 YRI
+sample_size 1 172
+pop_size 1 500000
+pop_define 2 CEU
+sample_size 2 172
+pop_size 2 250000
+pop_define 3 CHB
+sample_size 3 172
+pop_size 3 750000
+pop_define 4 BEB
+sample_size 4 172
+pop_size 4 1000000
+
+pop_event migration_rate "mig BEB->CHB" 4 3 0 0.00136172093665
+pop_event migration_rate "mig BEB->YRI" 4 1 0 0.005
+pop_event migration_rate "mig CEU->BEB" 2 4 0 0.005
+pop_event migration_rate "mig CEU->YRI" 2 1 0 0.01
+pop_event migration_rate "mig CHB->BEB" 3 4 0 0.00226891562673
+pop_event migration_rate "mig CHB->CEU" 3 2 0 1e-05
+pop_event migration_rate "mig CHB->YRI" 3 1 0 0.001
+pop_event migration_rate "mig YRI->CEU" 1 2 0 0.01
+pop_event migration_rate "mig YRI->CHB" 1 3 0 0.001
+pop_event migration_rate "mig YRI->BEB" 1 4 0 0.00728279079125
+pop_event exp_change_size2 "BEB exp Ne change" 4 1 50 1000000 50000
+pop_event exp_change_size2 "CHB exp Ne change" 3 1 75 750000 15000
+pop_event exp_change_size2 "YRI exp Ne change" 1 1 50 500000 40000
+pop_event migration_rate "mig CEU->CHB" 2 3 1 0.00061381604486
+pop_event exp_change_size2 "CEU exp Ne change" 2 1 50 250000 5039
+pop_event migration_rate "mig BEB->CHB" 4 3 4 1e-10
+pop_event migration_rate "mig YRI->CHB" 1 3 6 0.0001
+pop_event migration_rate "mig BEB->CEU" 4 2 10 0.0003
+pop_event migration_rate "mig BEB->YRI" 4 1 10 0.0002
+pop_event migration_rate "mig CEU->CHB" 2 3 10 0.005
+pop_event migration_rate "mig CEU->YRI" 2 1 10 0.00116816924107
+pop_event migration_rate "mig CHB->BEB" 3 4 10 1e-10
+pop_event migration_rate "mig CHB->CEU" 3 2 10 1e-05
+pop_event migration_rate "mig CHB->YRI" 3 1 10 0.000141006397915
+pop_event migration_rate "mig YRI->BEB" 1 4 10 0.0002
+pop_event migration_rate "mig YRI->CEU" 1 2 10 0.0005
+pop_event migration_rate "mig CEU->YRI" 2 1 28 0.0001
+pop_event migration_rate "mig BEB->CHB" 4 3 46 1e-10
+pop_event bottleneck "YRI bottleneck" 1 50 1e-10
+pop_event exp_change_size2 "BEB exp Ne change" 4 50 72 50000 4834
+pop_event exp_change_size2 "CEU exp Ne change" 2 50 300 5039 1500
+pop_event exp_change_size2 "YRI exp Ne change" 1 50 350 40000 8000
+pop_event migration_rate "mig YRI->CEU" 1 2 51 2.82017544024e-07
+pop_event bottleneck "BEB bottleneck" 4 67 1e-10
+pop_event admix "BEB admix" 4 2 68 0.44667558657
+pop_event exp_change_size2 "CHB exp Ne change" 3 75 300 15000 3000
+pop_event migration_rate "mig CEU->CHB" 2 3 94 1e-10
+pop_event migration_rate "mig BEB->CEU" 4 2 95 0.0001
+pop_event migration_rate "mig BEB->CEU" 4 2 100 0.0001
+pop_event migration_rate "mig BEB->YRI" 4 1 100 0.00269333810676
+pop_event migration_rate "mig CEU->BEB" 2 4 100 3.18160032659e-09
+pop_event migration_rate "mig CHB->BEB" 3 4 100 1e-10
+pop_event migration_rate "mig CHB->CEU" 3 2 100 0.0002
+pop_event migration_rate "mig CHB->YRI" 3 1 100 3.2668261552e-11
+pop_event migration_rate "mig CEU->BEB" 2 4 110 3.18160032659e-09
+pop_event bottleneck "BEB bottleneck" 4 149 1e-10
+pop_event split "BEB split" 3 4 150
+pop_event migration_rate "mig YRI->CHB" 1 3 189 1e-10
+pop_event exp_change_size2 "CEU exp Ne change" 2 300 2000 1500 1250
+pop_event exp_change_size2 "CHB exp Ne change" 3 300 900 3000 1000
+pop_event exp_change_size2 "YRI exp Ne change" 1 350 1087 8000 18397
+pop_event bottleneck "CEU bottleneck" 2 500 1e-10
+pop_event bottleneck "CHB bottleneck" 3 500 0.118659009739
+pop_event bottleneck "YRI bottleneck" 1 500 1e-10
+pop_event exp_change_size2 "YRI exp Ne change" 1 1087 3500 18397 10000
+pop_event bottleneck "CHB bottleneck" 3 1799 0.0904657845968
+pop_event split "CHB split" 2 3 1800
+pop_event bottleneck "CEU bottleneck" 2 2027 0.00282084598118
+pop_event split "CEU split" 1 2 2028
+pop_event change_size "YRI Ne change" 1 4000 29700
+pop_event bottleneck "YRI bottleneck" 1 5000 0.001
+pop_event change_size "YRI Ne change" 1 15000 15000
+
+pop_event migration_rate "no mig YRI->CEU" 1 2 2027 0
+pop_event migration_rate "no mig CEU->YRI" 2 1 2027 0
+pop_event migration_rate "no mig YRI->CHB" 1 3 2027 0
+pop_event migration_rate "no mig CHB->YRI" 3 1 2027 0
+pop_event migration_rate "no mig CEU->CHB" 2 3 2027 0
+pop_event migration_rate "no mig CHB->CEU" 3 2 2027 0
+pop_event migration_rate "no mig YRI->BEB" 1 4 149 0
+pop_event migration_rate "no mig BEB->YRI" 4 1 149 0
+pop_event migration_rate "no mig CEU->BEB" 2 4 149 0
+pop_event migration_rate "no mig BEB->CEU" 4 2 149 0
+pop_event migration_rate "no mig CHB->BEB" 3 4 149 0
+pop_event migration_rate "no mig BEB->CHB" 4 3 149 0

compute_intervals_stats.py

@@ -309,3 +309,4 @@ def compute_intervals_stats(args):
 
 if __name__ == '__main__':
     compute_intervals_stats(parse_args())
+

config/cms2_work_config.yml

@@ -8,11 +8,19 @@ terra:
     - [email protected]
 
   root_workflows:
-    cms2_make_min_sim_train_data:
+    cms2_best_model_make_min_sim_train_data:
       skip: False
       wdl: cms2_main.wdl
       synopsis: run sims and compute component stats with iSAFE on original model
       method_name: test-cosi2-method-01  # arbitrary until figure out how to create new methods in Terra workspace
+      config_name: cms2_best_model_make_min_sim_train_data
+      test_data: test.cms2_best_model_make_min_sim_train_data.wdl.json
+
+    cms2_make_min_sim_train_data:
+      skip: True
+      wdl: cms2_main.wdl
+      synopsis: run sims and compute component stats with iSAFE on original model
+      method_name: test-cosi2-method-01  # arbitrary until figure out how to create new methods in Terra workspace
       config_name: cms2_make_min_sim_train_data
       test_data: test.cms2_make_min_sim_train_data.wdl.json
 
@@ -65,9 +73,10 @@ terra:
       test_data: cms2_test_fetch.wdl.json
 
     cms2_construct_empirical_neutral_regions:
-      skip: True
+      skip: False
       wdl: empirical_neutral_regions.wdl
       synopsis: construct empirical neutral regions
       method_name: test-cosi2-method-01  # arbitrary until figure out how to create new methods in Terra workspace
       config_name: construct_empirical_neutral_regions
       test_data: test.construct_empirical_neutral_regions.wdl.json
+

construct_neutral_regions_list.py

@@ -395,6 +395,10 @@ def construct_genes_bed(genes_gff3, genes_pad_bp, chrom_sizes, genes_bed):
 def construct_pophumanscan_bed(pophumanscan_coords, pophumanscan_bed):
     execute(f"cat {pophumanscan_coords} | awk '(NR>1)' | cut -f 3-5 | sort -k1,1 -k2,2n | uniq > {pophumanscan_bed}")
 
+def construct_dgv_bed(dgv_bed):
+    execute(f'wget https://hgdownload.soe.ucsc.edu/gbdb/hg19/dgv/dgvSupporting.bb')
+    execute(f'bigBedToBed dgvSupporting.bb {dgv_bed}')
+
 def construct_neutral_regions_list(args):
 
     neut_reg_params = _json_loadf(args.empirical_neutral_regions_params)
@@ -414,11 +418,16 @@ def construct_neutral_regions_list(args):
     execute(f'bedtools subtract -a 05.full_chroms.sub_gaps.sub_genes.bed -b 06.pophumanscan.bed > '
             f'07.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.bed')
 
+    construct_dgv_bed(dgv_bed='08.dgv.bed')
+    execute(f'bedtools subtract -a 07.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.bed -b 08.dgv.bed > '
+            f'09.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.sub_dgv.bed')
+
+
     min_region_len_bp = neut_reg_params["min_region_len_bp"]
-    execute(f"awk '{{if($3-$2 >= {min_region_len_bp}) print}}' 07.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.bed "
-            f" > 08.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.len_filt.bed")
+    execute(f"awk '{{if($3-$2 >= {min_region_len_bp}) print}}' 09.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.sub_dgv.bed "
+            f" > 10.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.sub_dgv.len_filt.bed")
 
-    execute(f'cp 08.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.len_filt.bed {args.neutral_regions_bed}')
+    execute(f'cp 10.full_chroms.sub_gaps.sub_genes.sub_pophumanscan.sub_dgv.len_filt.bed {args.neutral_regions_bed}')
 
 if __name__ == '__main__':
     construct_neutral_regions_list(parse_args())

docker/common-tools/Dockerfile

@@ -24,7 +24,7 @@ RUN /opt/docker/install-miniconda.sh
 
 ENV PATH="$MINICONDA_PATH/bin:$PATH:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
 
-RUN conda install tar numpy scipy matplotlib pandas bokeh pytables h5py psutil tabix dominate bedtools bedops samtools bcftools && conda clean -a -y
+RUN conda install tar numpy scipy matplotlib pandas bokeh pytables h5py psutil tabix dominate bedtools bedops samtools bcftools ucsc-bigbedtobed && conda clean -a -y
 
 COPY Dockerfile /opt/docker/Dockerfile.save.txt
 COPY misc_utils.py /opt/pyutils/

docker/common-tools/install-miniconda.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 set -e -o pipefail
 
-MINICONDA_VERSION="4.10.3"
+MINICONDA_VERSION="4.11.0"
 MINICONDA_PY_VERSION="py38"
 MINICONDA_INSTALLER="Miniconda3-${MINICONDA_PY_VERSION}_${MINICONDA_VERSION}-Linux-x86_64.sh"
 #MINICONDA_URL="https://repo.anaconda.com/miniconda/${MINICONDA_INSTALLER}"

docker/main/install-miniconda.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 set -e -o pipefail
 
-MINICONDA_VERSION="4.8.3"
+MINICONDA_VERSION="4.11.0"
 MINICONDA_INSTALLER="Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh"
 MINICONDA_URL="https://repo.anaconda.com/miniconda/${MINICONDA_INSTALLER}"
 

tasks.wdl

@@ -47,8 +47,8 @@ task compute_one_pop_cms2_components {
   }
 
   runtime {
-    #docker: "quay.io/ilya_broad/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
-    docker: "quay.io/ilya_broad/cms:cms2-docker-component-stats-4fee1fcacb4f5a48cf188b753fed156e1bf3b9b2"  # selscan=1.3.0a09
+    #docker: "quay.io/broad_cms_ci/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
+    docker: "quay.io/broad_cms_ci/cms:cms2-docker-component-stats-aced0918ac0afd34f7cbb3031e3b044ac7e686cc"  # selscan=1.3.0a09
     preemptible: 3
     memory: "16 GB"
     cpu: 1
@@ -99,8 +99,8 @@ task compute_two_pop_cms2_components {
 
 # ** runtime
   runtime {
-    # docker: "quay.io/ilya_broad/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
-    docker: "quay.io/ilya_broad/cms:cms2-docker-component-stats-4fee1fcacb4f5a48cf188b753fed156e1bf3b9b2"  # selscan=1.3.0a09
+    # docker: "quay.io/broad_cms_ci/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
+    docker: "quay.io/broad_cms_ci/cms:cms2-docker-component-stats-aced0918ac0afd34f7cbb3031e3b044ac7e686cc"  # selscan=1.3.0a09
     preemptible: 3
     memory: "8 GB"
     cpu: 8
@@ -155,8 +155,8 @@ task compute_one_pop_bin_stats_for_normalization {
   }
 
   runtime {
-    docker: "quay.io/ilya_broad/cms:cms2-docker-component-stats-4fee1fcacb4f5a48cf188b753fed156e1bf3b9b2"  # selscan=1.3.0a09
-    #docker: "quay.io/ilya_broad/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
+    docker: "quay.io/broad_cms_ci/cms:cms2-docker-component-stats-aced0918ac0afd34f7cbb3031e3b044ac7e686cc"  # selscan=1.3.0a09
+    #docker: "quay.io/broad_cms_ci/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
     preemptible: 2
     memory: "8 GB"
     cpu: 1
@@ -210,8 +210,8 @@ task compute_two_pop_bin_stats_for_normalization {
   }
 
   runtime {
-    #docker: "quay.io/ilya_broad/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
-    docker: "quay.io/ilya_broad/cms:cms2-docker-component-stats-4fee1fcacb4f5a48cf188b753fed156e1bf3b9b2"  # selscan=1.3.0a09
+    #docker: "quay.io/broad_cms_ci/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
+    docker: "quay.io/broad_cms_ci/cms:cms2-docker-component-stats-aced0918ac0afd34f7cbb3031e3b044ac7e686cc"  # selscan=1.3.0a09
     preemptible: 2
     memory: "8 GB"
     cpu: 1
@@ -240,8 +240,8 @@ task normalize_and_collate_block {
     Pop sel_pop_used = inp.sel_pop
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms:cms2-docker-component-stats-4fee1fcacb4f5a48cf188b753fed156e1bf3b9b2"  # selscan=1.3.0a09
-    #docker: "quay.io/ilya_broad/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
+    docker: "quay.io/broad_cms_ci/cms:cms2-docker-component-stats-aced0918ac0afd34f7cbb3031e3b044ac7e686cc"  # selscan=1.3.0a09
+    #docker: "quay.io/broad_cms_ci/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
     memory: "1 GB"
     cpu: 1
     disks: "local-disk 10 HDD"
@@ -278,7 +278,7 @@ task collate_stats_and_metadata_for_sel_sims_block {
     File hapsets_metadata_tsv_gz = hapsets_metadata_tsv_gz_fname
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms:cms2-docker-component-stats-master--a785a15af758d87e457557ceb7528305d0beb42a"
+    docker: "quay.io/broad_cms_ci/cms:cms2-docker-component-stats-aced0918ac0afd34f7cbb3031e3b044ac7e686cc"
     memory: "4 GB"
     cpu: 1
     disks: "local-disk 25 HDD"
@@ -306,7 +306,7 @@ task create_tar_gz {
     File out_tar_gz = out_fname_tar_gz
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms@sha256:fc4825edda550ef203c917adb0b149cbcc82f0eeae34b516a02afaaab0eceac6"  # selscan=1.3.0a09
+    docker: "quay.io/broad_cms_ci/cms:wget-1544c1d7a6fbb36a7f0cfebf7aa332a6e52e767d"
     memory: "500 MB"
     cpu: 1
     disks: "local-disk 1 HDD"
@@ -343,7 +343,7 @@ task construct_pops_info_for_1KG {
     PopsInfo pops_info = read_json("${pops_info_fname}")["pops_info"]  # !UnverifiedStruct
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms@sha256:c8727e20ba0bc058c5c5596c4fad1ee23bc20c59f4f337ed62edb10e3a646010"  # selscan=1.3.0a09 with tabix
+    docker: "quay.io/broad_cms_ci/cms@sha256:c8727e20ba0bc058c5c5596c4fad1ee23bc20c59f4f337ed62edb10e3a646010"  # selscan=1.3.0a09 with tabix
     memory: "16 GB"
     cpu: 1
     disks: "local-disk 256 HDD"
@@ -392,7 +392,7 @@ task fetch_empirical_hapsets_from_1KG {
     Array[File]+ empirical_hapsets = glob("hapsets/*.hapset.tar.gz")
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms@sha256:c8727e20ba0bc058c5c5596c4fad1ee23bc20c59f4f337ed62edb10e3a646010"  # selscan=1.3.0a09 with tabix
+    docker: "quay.io/broad_cms_ci/cms@sha256:c8727e20ba0bc058c5c5596c4fad1ee23bc20c59f4f337ed62edb10e3a646010"  # selscan=1.3.0a09 with tabix
     memory: "16 GB"
     cpu: 1
     disks: "local-disk 256 HDD"
@@ -444,7 +444,7 @@ task call_neutral_region_explorer {
     String nre_results_url = read_string(nre_results_url_fname)
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms:webdriver-6dba18313775d137217c8a45c4bdd53d6b4e4441"
+    docker: "quay.io/broad_cms_ci/cms:webdriver-6dba18313775d137217c8a45c4bdd53d6b4e4441"
     memory: "4 GB"
     cpu: 1
     disks: "local-disk 32 HDD"
@@ -508,7 +508,7 @@ task fetch_file_from_url {
     String wget_cmd_used = wget_cmd_here
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms:wget-1544c1d7a6fbb36a7f0cfebf7aa332a6e52e767d"
+    docker: "quay.io/broad_cms_ci/cms:wget-1544c1d7a6fbb36a7f0cfebf7aa332a6e52e767d"
     memory: "4 GB"
     cpu: 1
     disks: "local-disk 32 HDD"
@@ -546,7 +546,7 @@ task compute_intervals_stats {
     File intervals_report_html = intervals_report_html_fname
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms:common-tools-69afd7403a40ccf2c1578be9f67d6e09b1143f22"
+    docker: "quay.io/broad_cms_ci/cms:common-tools-2b4d477113c453dc9e957c002f6665be20fd56fd"
     memory: "4 GB"
     cpu: 1
     disks: "local-disk 32 HDD"
@@ -591,7 +591,7 @@ task construct_neutral_regions_list {
     File empirical_neutral_regions_params_used_json = empirical_neutral_regions_params_json
   }
   runtime {
-    docker: "quay.io/ilya_broad/cms:common-tools-69afd7403a40ccf2c1578be9f67d6e09b1143f22"
+    docker: "quay.io/broad_cms_ci/cms:common-tools-2b4d477113c453dc9e957c002f6665be20fd56fd"
     memory: "4 GB"
     cpu: 1
     disks: "local-disk 32 HDD"