diff --git a/.github/workflows/candig-testing.yml b/.github/workflows/candig-testing.yml
index 7809b7bc1..fe0b4aed0 100644
--- a/.github/workflows/candig-testing.yml
+++ b/.github/workflows/candig-testing.yml
@@ -76,6 +76,6 @@ jobs:
         with:
           name: Post-build error log
           path: |
-                tmp/error.txt
+                tmp/progress.txt
                 tmp/container_logs.txt
                 tmp/vault_audit.log
diff --git a/.gitignore b/.gitignore
index 5d8e035ba..fd03f5829 100644
--- a/.gitignore
+++ b/.gitignore
@@ -50,3 +50,8 @@ pnpm-debug.log*
 
 # macOS-specific files
 .DS_Store
+
+# minio-related files
+lib/minio/access-key
+lib/minio/secret-key
+lib/minio/aws-credentials
diff --git a/Makefile b/Makefile
index 7b94d2cbd..fdcbc7d23 100644
--- a/Makefile
+++ b/Makefile
@@ -17,7 +17,6 @@ SHELL = bash
 CONDA = $(CONDA_INSTALL)/bin/conda
 CONDA_ENV_SETTINGS = $(CONDA_INSTALL)/etc/profile.d/conda.sh
 
-LOGFILE = tmp/progress.txt
 
 .PHONY: all
 all:
@@ -56,7 +55,7 @@ ifndef CONDA_INSTALL
 	echo "ERROR: Conda install location not specified. Do you have a .env?"
 	exit 1
 endif
-	echo "    started bin-conda" >> $(LOGFILE)
+	@printf "\nOutput of bin-conda:\n" | tee -a $(LOGFILE)
 ifeq ($(VENV_OS), linux)
 	curl -Lo bin/miniconda_install.sh \
 		https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
@@ -84,7 +83,6 @@ endif
 	$(CONDA) config --remove channels defaults
 	$(CONDA) config --add channels conda-forge
 	$(CONDA) config --set channel_priority strict
-	echo "    finished bin-conda" >> $(LOGFILE)
 
 
 #>>>
@@ -93,7 +91,7 @@ endif
 #<<<
 .PHONY: build-all
 build-all: mkdir
-	printf "Build started at `date '+%D %T'`.\n\n" >> $(ERRORLOG)
+	@printf "Build started at `date '+%D %T'`.\n\n" >> $(LOGFILE)
 	./pre-build-check.sh $(ARGS)
 
 # Setup the entire stack
@@ -132,15 +130,14 @@ build-images: #toil-docker
 
 #<<<
 build-%:
-	printf "\nOutput of build-$*: \n" >> $(ERRORLOG)
-	echo "    started build-$*" >> $(LOGFILE)
+	@printf "\nOutput of build-$*: \n" | tee -a $(LOGFILE)
 	source setup_hosts.sh
 	if [ -f lib/$*/$*_preflight.sh ]; then \
-	source lib/$*/$*_preflight.sh 2>&1 | tee -a $(ERRORLOG); \
+	source lib/$*/$*_preflight.sh 2>&1 | tee -a $(LOGFILE); \
 	fi
 	export SERVICE_NAME=$*; \
 	DOCKER_BUILDKIT=1 COMPOSE_DOCKER_CLI_BUILD=1 \
-	docker compose -f lib/candigv2/docker-compose.yml -f lib/$*/docker-compose.yml build $(BUILD_OPTS) 2>&1 | tee -a $(ERRORLOG)
+	docker compose -f lib/candigv2/docker-compose.yml -f lib/$*/docker-compose.yml build $(BUILD_OPTS) 2>&1 | tee -a $(LOGFILE)
 	echo "    finished build-$*" >> $(LOGFILE)
 
 
@@ -188,7 +185,6 @@ clean-authx:
 # Empties error and progress logs
 .PHONY: clean-logs
 clean-logs:
-	> $(ERRORLOG)
 	> $(LOGFILE)
 
 #>>>
@@ -259,7 +255,7 @@ clean-secrets:
 
 
 #>>>
-# remove all peristant volumes and local data
+# remove all persistent volumes and local data
 # make clean-volumes
 
 #<<<
@@ -289,20 +285,18 @@ containers=$(shell cat lib/$*/docker-compose.yml | yq -ojson '.services' | jq  '
 found=$(shell grep -ch $(containers) tmp/containers.txt)
 #<<<
 compose-%:
-	printf "\nOutput of compose-$*: \n" >> $(ERRORLOG)
-	echo "    started compose-$*" >> $(LOGFILE)
+	@printf "\nOutput of compose-$*: \n" | tee -a $(LOGFILE)
 	source setup_hosts.sh; \
 	python settings.py; source env.sh; \
 	export SERVICE_NAME=$*; \
-	docker compose -f lib/candigv2/docker-compose.yml -f lib/$*/docker-compose.yml --compatibility up -d 2>&1 | tee -a $(ERRORLOG)
+	docker compose -f lib/candigv2/docker-compose.yml -f lib/$*/docker-compose.yml --compatibility up -d 2>&1 | tee -a $(LOGFILE)
 	cat tmp/containers.txt
 	if [ $(found) -eq 0 ]; then \
 	echo $(containers) >> tmp/containers.txt; \
 	fi
 	if [ -f lib/$*/$*_setup.sh ]; then \
-	source lib/$*/$*_setup.sh 2>&1 | tee -a $(ERRORLOG); \
+	source lib/$*/$*_setup.sh 2>&1 | tee -a $(LOGFILE); \
 	fi
-	echo "    finished compose-$*" >> $(LOGFILE)
 
 
 #>>>
@@ -324,8 +318,7 @@ recompose-%:
 
 #<<<
 down-%:
-	printf "\nOutput of down-$*: \n" >> $(ERRORLOG)
-	echo "    started down-$*" >> $(LOGFILE)
+	@printf "\nOutput of down-$*: \n" | tee -a $(LOGFILE)
 	source setup_hosts.sh; \
 	export SERVICE_NAME=$*; \
 	docker compose -f lib/candigv2/docker-compose.yml -f lib/$*/docker-compose.yml --compatibility down 2>&1
@@ -360,7 +353,7 @@ docker-push:
 
 #<<<
 .PHONY: docker-secrets
-docker-secrets: mkdir authx-secrets data-secrets #minio-secrets
+docker-secrets: mkdir authx-secrets data-secrets
 
 
 data-secrets: mkdir
@@ -383,11 +376,12 @@ authx-secrets: mkdir
 
 minio-secrets: mkdir
 	@echo "making minio secrets"
-	@echo $(DEFAULT_ADMIN_USER) > tmp/secrets/minio-access-key
+	@echo $(DEFAULT_ADMIN_USER) > lib/minio/access-key
 	$(MAKE) secret-minio-secret-key
-	@echo '[default]' > tmp/secrets/aws-credentials
-	@echo "aws_access_key_id=`cat tmp/secrets/minio-access-key`" >> tmp/secrets/aws-credentials
-	@echo "aws_secret_access_key=`cat tmp/secrets/minio-secret-key`" >> tmp/secrets/aws-credentials
+	mv tmp/secrets/minio-secret-key lib/minio/secret-key
+	@echo '[default]' > lib/minio/aws-credentials
+	@echo "aws_access_key_id=`cat lib/minio/access-key`" >> lib/minio/aws-credentials
+	@echo "aws_secret_access_key=`cat lib/minio/secret-key`" >> lib/minio/aws-credentials
 
 
 #>>>
@@ -399,8 +393,6 @@ minio-secrets: mkdir
 docker-volumes:
 	docker volume create grafana-data --label candigv2=volume
 	docker volume create jupyter-data --label candigv2=volume
-	# docker volume create minio-config --label candigv2=volume
-	# docker volume create minio-data $(MINIO_VOLUME_OPT) --label candigv2=volume
 	docker volume create prometheus-data --label candigv2=volume
 	docker volume create toil-jobstore --label candigv2=volume
 	docker volume create keycloak-data --label candigv2=volume
@@ -425,6 +417,17 @@ init-authx: mkdir
 	$(foreach MODULE, $(CANDIG_AUTH_MODULES), $(MAKE) build-$(MODULE); $(MAKE) compose-$(MODULE); python settings.py;)
 
 
+#>>>
+# create a minio container (that won't be removed as part of clean-all)
+# make init-minio
+
+#<<<
+init-minio: minio-secrets
+	docker volume create minio-config
+	docker volume create minio-data $(MINIO_VOLUME_OPT)
+	docker compose -f lib/candigv2/docker-compose.yml -f lib/minio/docker-compose.yml --compatibility up -d 2>&1 | tee -a $(LOGFILE)
+
+
 #>>>
 # initialize conda environment
 # make init-conda
@@ -432,7 +435,7 @@ init-authx: mkdir
 #<<<
 .PHONY: init-conda
 init-conda:
-	echo "    started init-conda" >> $(LOGFILE)
+	@printf "\nOutput of init-conda: \n" | tee -a $(LOGFILE)
 	# source conda's script to be safe, so the conda command is found
 	source $(CONDA_ENV_SETTINGS) \
 		&& $(CONDA) create -y -n $(VENV_NAME) python=$(VENV_PYTHON) pip=$(VENV_PIP)
@@ -445,7 +448,6 @@ init-conda:
 #@echo "Load local conda: source bin/miniconda3/etc/profile.d/conda.sh"
 #@echo "Activate conda env: conda activate $(VENV_NAME)"
 #@echo "Install requirements: pip install -U -r etc/venv/requirements.txt"
-	echo "    finished init-conda" >> $(LOGFILE)
 
 
 #>>>
@@ -494,7 +496,7 @@ secret-%:
 #<<<
 .PHONY: toil-docker
 toil-docker:
-	echo "    started toil-docker" >> $(LOGFILE)
+	@printf "\nOutput of toil-docker: \n" | tee -a $(LOGFILE)
 	VIRTUAL_ENV=1 DOCKER_BUILDKIT=1 COMPOSE_DOCKER_CLI_BUILD=1 TOIL_DOCKER_REGISTRY=$(DOCKER_REGISTRY) \
 	$(MAKE) -C lib/toil/toil-docker docker
 	$(foreach MODULE,$(TOIL_MODULES), \
@@ -504,7 +506,6 @@ toil-docker:
 		docker tag $(DOCKER_REGISTRY)/$(MODULE):$(TOIL_VERSION) \
 		$(DOCKER_REGISTRY)/$(MODULE):latest;)
 	$(foreach MODULE, $(TOIL_MODULES), docker push $(DOCKER_REGISTRY)/$(MODULE):latest;)
-	echo "    finished toil-docker" >> $(LOGFILE)
 
 
 #>>>
diff --git a/docs/astro.config.mjs b/docs/astro.config.mjs
index 241af8d1c..b8558f944 100644
--- a/docs/astro.config.mjs
+++ b/docs/astro.config.mjs
@@ -41,31 +41,31 @@ export default defineConfig({
         }),
         starlightOpenAPI([
             {
-                base: 'technical/ingest',
+                base: 'technical/ingest-api',
                 label: 'ingest api',
                 schema: 'https://raw.githubusercontent.com/CanDIG/candigv2-ingest/refs/heads/develop/ingest_openapi.yaml',
                 collapsed: true
             },
             {
-                base: 'technical/query',
+                base: 'technical/query-api',
                 label: 'query api',
                 schema: 'https://raw.githubusercontent.com/CanDIG/candigv2-query/refs/heads/stable/query_server/openapi.yaml',
                 collapsed: true
             },
             {
-                base: 'technical/katsu',
+                base: 'technical/katsu-api',
                 label: 'katsu api',
                 schema: 'https://raw.githubusercontent.com/CanDIG/katsu/refs/heads/stable/chord_metadata_service/mohpackets/docs/schemas/schema.yml',
                 collapsed: true
             },
             {
-                base: 'technical/htsget/drs',
+                base: 'technical/htsget/drs-api',
                 label: 'htsget drs api',
                 schema: 'https://raw.githubusercontent.com/CanDIG/htsget_app/refs/heads/stable/htsget_server/drs_openapi.yaml',
                 collapsed: true
             },
             {
-                base: 'technical/htsget/beacon',
+                base: 'technical/htsget/beacon-api',
                 label: 'htsget beacon api',
                 schema: 'https://raw.githubusercontent.com/CanDIG/htsget_app/refs/heads/stable/htsget_server/beacon_openapi.yaml',
                 collapsed: true
@@ -76,6 +76,12 @@ export default defineConfig({
                 schema: 'https://raw.githubusercontent.com/CanDIG/htsget_app/refs/heads/stable/htsget_server/htsget_openapi.yaml',
                 collapsed: true
             },
+	    {
+                base: 'technical/federation-api',
+                label: 'htsget operations api',
+                schema: 'https://raw.githubusercontent.com/CanDIG/federation_service/refs/heads/develop/candig_federation/federation.yaml',
+                collapsed: true
+            },
         ])
     ],
     sidebar: [
@@ -131,4 +137,4 @@ export default defineConfig({
         },
     ],
 		})]
-});
\ No newline at end of file
+});
diff --git a/docs/src/content/docs/ingest/ingest-help.mdx b/docs/src/content/docs/ingest/ingest-help.mdx
index 0d4a664ec..a10817c53 100644
--- a/docs/src/content/docs/ingest/ingest-help.mdx
+++ b/docs/src/content/docs/ingest/ingest-help.mdx
@@ -95,7 +95,7 @@ If you receive an error when using the `/ingest/genomic` endpoint something like
 
 This means that the token used by ingest to submit to hts-get has expired. At the moment this happens after 30 minutes. Get a fresh token and try again.
 
-### What if I need to delete or edit data that I already ingested into the system?
+## What if I need to delete or edit data that I already ingested into the system?
 
 Currently, there is no way to edit data that is already ingested into CanDIG. To change any data, the data must be deleted and re-ingested. Follow the steps below in order to delete data in CanDIG.
 
@@ -125,7 +125,7 @@ This token should be kept secure, it lasts for 30 mins
 
 ```bash
 curl --request DELETE \
---url $CANDIG_URL'/katsu/v2/ingest/program/$PROGRAM_ID/' \
+--url $CANDIG_URL'/katsu/v3/ingest/program/$PROGRAM_ID/' \
 -H 'accept: application/json' \
 -H 'Content-Type: application/json' \
 -H 'Authorization: Bearer '$TOKEN
@@ -179,7 +179,3 @@ When attempting clinical data ingest into katsu, if you get a response such as b
 ```
 
 It means you have not yet registered your program before ingesting. Please follow the instructions in [Register Programs](register-programs/) to submit a program authorization before attempting clinical ingest again.
-
-:::danger
-This token should be kept secure, it lasts for 30 mins.
-:::
diff --git a/etc/env/example.env b/etc/env/example.env
index aa3dfb893..7d4b3c8b2 100644
--- a/etc/env/example.env
+++ b/etc/env/example.env
@@ -3,7 +3,7 @@
 
 # site options
 CANDIG_MODULES=logging keycloak vault redis postgres htsget katsu query tyk opa federation candig-ingest candig-data-portal
-    #minio drs-server wes-server monitoring
+    #drs-server wes-server monitoring
 CANDIG_AUTH_MODULES=keycloak vault tyk opa federation
 CANDIG_DATA_MODULES=keycloak vault redis postgres logging
 
@@ -301,7 +301,9 @@ CANDIG_DATA_PORTAL_PRIVATE_URL=http://candig-data-portal:3000
 TOKEN_PATH = ${PWD}/Vault-Helper-Tool/token.txt
 PROGRESS_FILE = ${PWD}/tmp/progress.txt
 
-# error logging
-ERRORLOG=tmp/error.txt
+# install logging
+LOGFILE = tmp/progress.txt
 
 CONDA_INSTALL=bin/miniconda3
+
+COMPOSE_IGNORE_ORPHANS=True
diff --git a/etc/tests/test_integration.py b/etc/tests/test_integration.py
index 0803fd4d2..d486455a3 100644
--- a/etc/tests/test_integration.py
+++ b/etc/tests/test_integration.py
@@ -443,6 +443,7 @@ def test_ingest_not_admin_katsu():
     while response.status_code == 200 and "status" in response.json():
         time.sleep(2)
         response = requests.get(f"{ENV['CANDIG_URL']}/ingest/status/{queue_id}", headers=headers)
+    print(response.text)
     assert len(response.json()[f"{ENV['CANDIG_ENV']['CANDIG_SITE_LOCATION']}-SYNTH_01"]["errors"]) == 0
     assert len(response.json()[f"{ENV['CANDIG_ENV']['CANDIG_SITE_LOCATION']}-SYNTH_01"]["results"]) == 13
     katsu_response = requests.get(f"{ENV['CANDIG_ENV']['KATSU_INGEST_URL']}/v3/discovery/programs/")
@@ -1077,6 +1078,7 @@ def test_query_donor_search():
             assert summary_stats[category][value] == expected_response[category][value]
 
 
+# Can we can find donors by querying a specific region of the genome?
 def test_query_genomic():
     # tests that a request sent via query to htsget-beacon properly prunes the data
     token = get_token(username=ENV['CANDIG_NOT_ADMIN2_USER'],
@@ -1150,29 +1152,8 @@ def test_query_genomic():
                 print(f"{donor["program_id"]}: {donor["submitter_donor_id"]}")
     assert response and len(response.json()["results"]) == 1
 
-    # token = get_token(username=ENV['CANDIG_NOT_ADMIN_USER'],
-    #                   password=ENV['CANDIG_NOT_ADMIN_PASSWORD'])
-    # headers = {
-    #     "Authorization": f"Bearer {token}",
-    #     "Content-Type": "application/json; charset=utf-8",
-    # }
-    # params = {
-    #     "gene": "TP53",
-    #     "assembly": "hg38"
-    # }
-    # response = requests.get(
-    #     f"{ENV['CANDIG_URL']}/query/query", headers=headers, params=params
-    # )
-    # pprint.pprint(response.json())
-    # if len(response.json()["results"]) != 0:
-    #     print(f"\n\nExpected 0 results from the genomic query using gene name 'TP53' but got {len(response.json()["results"])}")
-    #     if len(response.json()["results"]) > 0:
-    #         print("Got results from:")
-    #         for donor in response.json()["results"]:
-    #             print(f"{donor["program_id"]}: {donor["submitter_donor_id"]}")
-    # assert response and len(response.json()["results"]) == 0
-
 
+# Can we use a discovery query to get counts of donors we do not have access to?
 def test_query_discovery():
     katsu_response = requests.get(
         f"{ENV['CANDIG_ENV']['KATSU_INGEST_URL']}/v3/discovery/programs/"
@@ -1203,6 +1184,18 @@ def test_query_discovery():
                 assert field in query_response["site"]["required_but_missing"][category]
 
 
+# Can we check how many donors have genomics data?
+def test_query_completeness():
+    query_response = requests.get(
+        f"{ENV['CANDIG_ENV']['QUERY_INTERNAL_URL']}/genomic_completeness").json()
+    pprint.pprint(query_response)
+    # Verify that the synthetic data shows up
+    assert "LOCAL-SYNTH_01" in query_response
+    assert query_response["LOCAL-SYNTH_01"]["genomes"] == 6
+    assert "LOCAL-SYNTH_02" in query_response
+    assert query_response["LOCAL-SYNTH_02"]["genomes"] == 5
+
+
 def test_clean_up():
     clean_up_program(f"{ENV['CANDIG_ENV']['CANDIG_SITE_LOCATION']}-SYNTH_01")
     clean_up_program(f"{ENV['CANDIG_ENV']['CANDIG_SITE_LOCATION']}-SYNTH_02")
diff --git a/lib/candigv2/docker-compose.yml b/lib/candigv2/docker-compose.yml
index d9aa723d5..4669f8547 100644
--- a/lib/candigv2/docker-compose.yml
+++ b/lib/candigv2/docker-compose.yml
@@ -1,8 +1,4 @@
 volumes:
-  # minio-data:
-  #   external: true
-  # minio-config:
-  #   external: true
   toil-jobstore:
     external: true
   prometheus-data:
@@ -31,14 +27,6 @@ secrets:
     file: $PWD/tmp/postgres/db-secret
     labels:
       - "candigv2=secret"
-  # minio-access-key:
-  #   file: $PWD/tmp/secrets/minio-access-key
-  #   labels:
-  #     - "candigv2=secret"
-  # minio-secret-key:
-  #   file: $PWD/tmp/secrets/minio-secret-key
-  #   labels:
-  #     - "candigv2=secret"
   wes-dependency-resolver:
     file: $PWD/etc/yml/${WES_DEPENDENCY_RESOLVER}.yml
     labels:
diff --git a/lib/minio/docker-compose.yml b/lib/minio/docker-compose.yml
index fbb70ae37..af66340fd 100644
--- a/lib/minio/docker-compose.yml
+++ b/lib/minio/docker-compose.yml
@@ -1,8 +1,16 @@
+volumes:
+  minio-data:
+    external: true
+  minio-config:
+    external: true
+secrets:
+  minio-access-key:
+    file: $PWD/lib/minio/access-key
+  minio-secret-key:
+    file: $PWD/lib/minio/secret-key
 services:
   minio:
     image: minio/minio:${MINIO_VERSION:-latest}
-    labels:
-      - "candigv2=minio"
     volumes:
       - minio-data:/data
       - minio-config:/root/.minio
diff --git a/lib/toil/docker-compose.yml b/lib/toil/docker-compose.yml
index afbef2209..c65008485 100644
--- a/lib/toil/docker-compose.yml
+++ b/lib/toil/docker-compose.yml
@@ -1,3 +1,10 @@
+secrets:
+  minio-access-key:
+    file: $PWD/lib/minio/access-key
+  minio-secret-key:
+    file: $PWD/lib/minio/secret-key
+  aws-credentials:
+    file: $PWD/lib/minio/aws-credentials
 services:
   toil-server:
     image: ${DOCKER_REGISTRY}/toil:${TOIL_VERSION:-latest}
diff --git a/lib/wes-server/docker-compose.yml b/lib/wes-server/docker-compose.yml
index 0d858e112..72943f6ff 100644
--- a/lib/wes-server/docker-compose.yml
+++ b/lib/wes-server/docker-compose.yml
@@ -1,3 +1,10 @@
+secrets:
+  minio-access-key:
+    file: $PWD/lib/minio/access-key
+  minio-secret-key:
+    file: $PWD/lib/minio/secret-key
+  aws-credentials:
+    file: $PWD/lib/minio/aws-credentials
 services:
   wes-server:
     build:
diff --git a/post_build.sh b/post_build.sh
index 2819810eb..b00ff32e4 100755
--- a/post_build.sh
+++ b/post_build.sh
@@ -6,7 +6,8 @@
 # Also prints out all relevant logs from the error logging file (i.e., all lines
 # that contain the phrases 'error' or 'warn').
 
-source <(grep --color=never "ERRORLOG" .env)
+python settings.py
+source env.sh
 
 RED='\033[0;31m'
 YELLOW='\033[1;33m'
@@ -16,7 +17,8 @@ DEFAULT='\033[0m'
 
 function print_module_logs() {
 	MODULE=$1
-	BUILD_LINE=$(grep -n build-${MODULE} ${ERRORLOG} | tail -1 | cut -d ':' -f 1)
+	output=""
+	BUILD_LINE=$(grep -n build-${MODULE} ${LOGFILE} | tail -1 | cut -d ':' -f 1)
 	if [[ $BUILD_LINE != "" ]]; then
 		LNO=$BUILD_LINE
 		while read -r LINE; do
@@ -24,13 +26,13 @@ function print_module_logs() {
 				break
 			else
 				if [[ ${LINE} =~ .*([Ee]rror|[Ww]arn).* ]]; then
-					printf "${GREEN}${LNO}${DEFAULT}	${LINE}\n"
+					output="${output}${GREEN}${LNO}${DEFAULT}	${LINE}\n"
 				fi
 			fi
 			LNO=$((LNO+1))
-		done < <(tail -n "+$((BUILD_LINE + 1))" $ERRORLOG)
+		done < <(tail -n "+$((BUILD_LINE + 1))" $LOGFILE)
 	fi
-	COMPOSE_LINE=$(grep -n compose-${MODULE} ${ERRORLOG} | tail -1 | cut -d ':' -f 1)
+	COMPOSE_LINE=$(grep -n compose-${MODULE} ${LOGFILE} | tail -1 | cut -d ':' -f 1)
 	if [[ $COMPOSE_LINE != "" ]]; then
 		LNO=$COMPOSE_LINE
 		while read -r LINE; do
@@ -38,41 +40,54 @@ function print_module_logs() {
 				break
 			else
 				if [[ ${LINE} =~ .*([Ee]rror|[Ww]arn).* ]]; then
-					printf "${GREEN}${LNO}${DEFAULT}	${LINE}\n"
+					output="${output}${GREEN}${LNO}${DEFAULT}	${LINE}\n"
 				fi
 			fi
 			LNO=$((LNO+1))
-		done < <(tail -n "+$((COMPOSE_LINE+1))" $ERRORLOG)
+		done < <(tail -n "+$((COMPOSE_LINE+1))" $LOGFILE)
+	fi
+	if [[ $output != "" ]]; then
+		printf "\n\n${RED}Error logs for ${MODULE}:\n--------------------\n${DEFAULT}"
+		printf "${output}"
+		printf "${RED}--------------------\n${DEFAULT}\n"
 	fi
 }
 
 MODULES=$(cat .env | grep CANDIG_MODULES | cut -c 16- | cut -d '#' -f 1)
 ALL_MODULES="${MODULES}"
 
-SERVICE_COUNT=0
+EXPECTED_CONTAINERS=""
 for MODULE in $ALL_MODULES; do
+  services=$(cat lib/$MODULE/docker-compose.yml | yq -ojson '.services' | jq  'keys' | jq -r @sh | sed s/^\'/candigv2_/g | sed s/\'$/_1/g | sed "s/\'\ \'/_1\\ candigv2_/g" | sed "s/'\\s'/_1\\ candigv2_/g")
+  EXPECTED_CONTAINERS=$(echo $EXPECTED_CONTAINERS $services)
   sc=$(cat lib/$MODULE/docker-compose.yml | yq -ojson '.services' | jq  'keys' | jq -r @sh | wc -w | tr -d ' ')
-  SERVICE_COUNT=`expr $SERVICE_COUNT + $sc`
 done
 
-RUNNING_MODULES=$(docker ps --format "{{.Names}}")
+EXPECTED_COUNT=$(echo $EXPECTED_CONTAINERS | wc -w)
+
+RUNNING_CONTAINERS=$(docker ps --format "{{.Names}}")
+RUNNING_COUNT=$(echo $RUNNING_CONTAINERS | wc -w)
 
-if [ $(docker ps -q | wc -l) == $SERVICE_COUNT ]
+# figure out any containers that should've been there but aren't
+for i in $EXPECTED_CONTAINERS
+do
+	[[ ! $RUNNING_CONTAINERS =~ $i  ]] && MISSING_CONTAINERS="${MISSING_CONTAINERS:+${MISSING_CONTAINERS} }$i"
+done
+# echo expected: $EXPECTED_CONTAINERS
+# echo running: $RUNNING_CONTAINERS
+# echo missing: $MISSING_CONTAINERS
+if [[ $(echo $MISSING_CONTAINERS | wc -w | tr -d ' ') == "0"  ]]
 then
 	for MODULE in $ALL_MODULES; do
-		printf "\n\n${BLUE}Error logs for ${MODULE}:\n--------------------\n${DEFAULT}"
-		print_module_logs $MODULE
-		printf "${BLUE}--------------------\n${DEFAULT}"
+		print_module_logs $MODULE $COLOR
 	done
-	echo -e "${GREEN}Number of expected CanDIG services matches number of containers running!${DEFAULT} Potentially useful error log segments listed above for debugging."
+	echo -e "${GREEN}Number of expected CanDIG services matches number of containers running!${DEFAULT} Lines above are in ${LOGFILE} and may be helpful for debugging."
  	exit 0
 else
 	for MODULE in $ALL_MODULES; do
-		printf "\n\n${RED}Error logs for ${MODULE}:\n--------------------\n${DEFAULT}"
 		print_module_logs $MODULE
-		printf "${RED}--------------------\n${DEFAULT}"
 	done
-	echo -e "${RED}WARNING: ${YELLOW}The number of CanDIG containers running does not match the number of expected services.\nRunning: ${BLUE}$(docker ps -q | wc -l) ${YELLOW}Expected: ${BLUE}${SERVICE_COUNT}
-${DEFAULT}Check your build/docker logs. Potentially offending service logs shown above. View ${ERRORLOG} for more information."
+	echo -e "${RED}WARNING: ${YELLOW}Some containers that are expected to be running are missing:\n${MISSING_CONTAINERS}
+${DEFAULT}Lines above are in ${LOGFILE} and may be helpful for debugging."
 	exit 1
 fi
diff --git a/settings.py b/settings.py
index 476627d79..f09644bf5 100755
--- a/settings.py
+++ b/settings.py
@@ -41,6 +41,7 @@ def get_env_value(key):
 
 def get_env():
     vars = {}
+    vars["LOGFILE"] = get_env_value("LOGFILE")
     vars["CANDIG_URL"] = get_env_value("TYK_LOGIN_TARGET_URL")
     vars["CANDIG_CLIENT_ID"] = get_env_value("KEYCLOAK_CLIENT_ID")
     vars["KEYCLOAK_PUBLIC_URL"] = get_env_value("KEYCLOAK_PUBLIC_URL")