## This script contains all commands executed in the PROJECT fmvblq and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run)
echo '*******************Reproducing analysis of PROJECT fmvblq / ASAP33**********************'
echo '***************************************************************************************'

## CONFIGURATION (edit below to match your machine; lines until the separator)
export ASAP_PROJECTS_DIR=/asap_projects ## change this to write analysis results there (there will be subdirectory for each project key).
export LOOM_DIR=$ASAP_PROJECTS_DIR/loom_files
export ASAP_DATA_DB_HOST=localhost; export ASAP_DATA_DB_PORT=5432
export PSQL_DIR=/usr/pgsql-10/bin

## =========================================================

export PROJECT_DIR=$ASAP_PROJECTS_DIR/fmvblq
## Pull Docker images (must run before any docker run in this script)

docker pull fabdavid/asap_run:v5

## Host LOOM staging directory (inside Docker volume)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $LOOM_DIR; chmod 777 $LOOM_DIR"

echo 'This project is PUBLIC => Nothing to do'

## Local PostgreSQL: create ASAP data database and load dump if missing
if ! psql -lqt | cut -d \| -f 1 | grep -qw asap_data_v5; then echo 'Create database asap_data_v5'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v5'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v5; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v5.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v5'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v5.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v5; fi

## Project directory on the shared volume
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR"

## Step output directories (one folder per pipeline step that has runs)
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/markers/ && mkdir -p $PROJECT_DIR/marker_enrich/"

## Parsed LOOM file (public: wget; private: place file then symlink as below)
echo 'Loading parsed Loom file...'
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/fmvblq/get_file?filename=parsing/output.loom'"

## Re-execute each recorded run (parsing step is skipped; LOOM is already in place)


## ----------------------------------------------------------------
## Run 73693  Normalization  (Normalization #1 asap_seurat)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/normalization/73693/"

## Running Normalization [73693] [Normalization #1 asap_seurat] (input_matrix:parsing)
echo '-> Running Normalization [73693] [Normalization #1 asap_seurat] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_73693 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/normalization/73693/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000  1> /data/asap2/users/1/fmvblq/normalization/73693/exec.out 2> /data/asap2/users/1/fmvblq/normalization/73693/exec.err'"


## ----------------------------------------------------------------
## Run 168062  Find markers  (Find markers #1 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/168062/"

## Running Find markers [168062] [Find markers #1 asap_markers] ()
echo '-> Running Find markers [168062] [Find markers #1 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_168062 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/168062 --iAnnot /col_attrs/annotation --id 470935  1> /data/asap2/users/1/fmvblq/markers/168062/exec.out 2> /data/asap2/users/1/fmvblq/markers/168062/exec.err'"


## ----------------------------------------------------------------
## Run 168063  Marker enrichment  (Marker enrichment #2 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/168063/"

## Running Marker enrichment [168063] [Marker enrichment #2 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [168063] [Marker enrichment #2 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_168063 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/fmvblq/markers/168062 -o /data/asap2/users/1/fmvblq/markers/168063 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/fmvblq/markers/168063/exec.out 2> /data/asap2/users/1/fmvblq/markers/168063/exec.err'"


## ----------------------------------------------------------------
## Run 216964  Find markers  (Find markers #2 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/216964/"

## Running Find markers [216964] [Find markers #2 asap_markers] ()
echo '-> Running Find markers [216964] [Find markers #2 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_216964 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/216964 --iAnnot /col_attrs/Clustering_Leiden_resolution_18.0 --id 470922 --is_count_table  1> /data/asap2/users/1/fmvblq/markers/216964/exec.out 2> /data/asap2/users/1/fmvblq/markers/216964/exec.err'"


## ----------------------------------------------------------------
## Run 216965  Marker enrichment  (Marker enrichment #3 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/216965/"

## Running Marker enrichment [216965] [Marker enrichment #3 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [216965] [Marker enrichment #3 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_216965 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/fmvblq/markers/216964 -o /data/asap2/users/1/fmvblq/markers/216965 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/fmvblq/markers/216965/exec.out 2> /data/asap2/users/1/fmvblq/markers/216965/exec.err'"


## ----------------------------------------------------------------
## Run 249755  Find markers  (Find markers #3 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/249755/"

## Running Find markers [249755] [Find markers #3 asap_markers] ()
echo '-> Running Find markers [249755] [Find markers #3 asap_markers] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_249755 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/249755 --iAnnot /col_attrs/annotation_broad --id 470900 --is_count_table  1> /data/asap2/users/1/fmvblq/markers/249755/exec.out 2> /data/asap2/users/1/fmvblq/markers/249755/exec.err'"


## ----------------------------------------------------------------
## Run 249756  Marker enrichment  (Marker enrichment #4 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/249756/"

## Running Marker enrichment [249756] [Marker enrichment #4 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [249756] [Marker enrichment #4 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_249756 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/fmvblq/markers/249755 -o /data/asap2/users/1/fmvblq/markers/249756 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/fmvblq/markers/249756/exec.out 2> /data/asap2/users/1/fmvblq/markers/249756/exec.err'"


## ----------------------------------------------------------------
## Run 343922  Find markers  (Find markers #4 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/343922/"

## Running Find markers [343922] [Find markers #4 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [343922] [Find markers #4 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_343922 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/343922 --iAnnot /col_attrs/annotation --id 470935 --is_count_table true  1> /data/asap2/users/1/fmvblq/markers/343922/exec.out 2> /data/asap2/users/1/fmvblq/markers/343922/exec.err'"


## ----------------------------------------------------------------
## Run 343923  Marker enrichment  (Marker enrichment #5 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/343923/"

## Running Marker enrichment [343923] [Marker enrichment #5 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [343923] [Marker enrichment #5 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_343923 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/fmvblq/markers/343922 -o /data/asap2/users/1/fmvblq/markers/343923 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/fmvblq/markers/343923/exec.out 2> /data/asap2/users/1/fmvblq/markers/343923/exec.err'"


## ----------------------------------------------------------------
## Run 395188  Find markers  (Find markers #5 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/395188/"

## Running Find markers [395188] [Find markers #5 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [395188] [Find markers #5 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_395188 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/395188 --iAnnot /col_attrs/ClusterID --id 470901 --is_count_table true  1> /data/asap2/users/1/fmvblq/markers/395188/exec.out 2> /data/asap2/users/1/fmvblq/markers/395188/exec.err'"


## ----------------------------------------------------------------
## Run 395189  Marker enrichment  (Marker enrichment #6 asap_marker_enrichment)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/395189/"

## Running Marker enrichment [395189] [Marker enrichment #6 asap_marker_enrichment] ()
echo '-> Running Marker enrichment [395189] [Marker enrichment #6 asap_marker_enrichment] ()'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_395189 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/1/fmvblq/markers/395188 -o /data/asap2/users/1/fmvblq/markers/395189 --genesets 671,672,673,2371,3138 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5  1> /data/asap2/users/1/fmvblq/markers/395189/exec.out 2> /data/asap2/users/1/fmvblq/markers/395189/exec.err'"


## ----------------------------------------------------------------
## Run 559282  Find markers  (Find markers #6 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/559282/"

## Running Find markers [559282] [Find markers #6 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [559282] [Find markers #6 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_559282 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/559282 --iAnnot /col_attrs/Clustering_Annotation --id 470923 --is_count_table true  1> /data/asap2/users/1/fmvblq/markers/559282/exec.out 2> /data/asap2/users/1/fmvblq/markers/559282/exec.err'"


## ----------------------------------------------------------------
## Run 559296  Find markers  (Find markers #7 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/559296/"

## Running Find markers [559296] [Find markers #7 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [559296] [Find markers #7 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_559296 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR   fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/559296 --iAnnot /col_attrs/S_annotation --id 470957 --is_count_table true  1> /data/asap2/users/1/fmvblq/markers/559296/exec.out 2> /data/asap2/users/1/fmvblq/markers/559296/exec.err'"


## ----------------------------------------------------------------
## Run 748501  Find markers  (Find markers #8 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/748501/"

## Running Find markers [748501] [Find markers #8 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [748501] [Find markers #8 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_748501 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR  fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/748501 --iAnnot /col_attrs/tissue --id 470931 --is_count_table true  1> /data/asap2/users/1/fmvblq/markers/748501/exec.out 2> /data/asap2/users/1/fmvblq/markers/748501/exec.err'"


## ----------------------------------------------------------------
## Run 753768  Find markers  (Find markers #9 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/753768/"

## Running Find markers [753768] [Find markers #9 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [753768] [Find markers #9 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_753768 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR  fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/753768 --iAnnot /col_attrs/sex --id 470952 --is_count_table true  1> /data/asap2/users/1/fmvblq/markers/753768/exec.out 2> /data/asap2/users/1/fmvblq/markers/753768/exec.err'"


## ----------------------------------------------------------------
## Run 761545  Find markers  (Find markers #10 asap_markers)
## ----------------------------------------------------------------

## Ensure output directory exists
docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/761545/"

## Running Find markers [761545] [Find markers #10 asap_markers] (input_matrix:parsing)
echo '-> Running Find markers [761545] [Find markers #10 asap_markers] (input_matrix:parsing)'

## Command
docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_761545 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR  fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/1/fmvblq/parsing/output.loom -o /data/asap2/users/1/fmvblq/markers/761545 --iAnnot /col_attrs/annotation__ontology_id --id 470898 --is_count_table true  1> /data/asap2/users/1/fmvblq/markers/761545/exec.out 2> /data/asap2/users/1/fmvblq/markers/761545/exec.err'"