## This script contains all commands executed in the PROJECT ak9s4r and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run) echo '*******************Reproducing analysis of PROJECT ak9s4r / ASAP6**********************' 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/ak9s4r ## 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/gene_filtering/ && mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/dim_reduction/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/de/ && mkdir -p $PROJECT_DIR/ge/ && mkdir -p $PROJECT_DIR/cell_filtering/ && mkdir -p $PROJECT_DIR/cell_selection/ && mkdir -p $PROJECT_DIR/scaling/" ## 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/ak9s4r/get_file?filename=parsing/output.loom'" ## Re-execute each recorded run (parsing step is skipped; LOOM is already in place) ## ---------------------------------------------------------------- ## Run 14490 Cell filtering (Cell filtering #1 qc_plots) ## ---------------------------------------------------------------- ## 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/cell_filtering/14490/" ## writing file $PROJECT_DIR/cell_filtering/14490/discarded_cols.json echo '-> writing file $PROJECT_DIR/cell_filtering/14490/discarded_cols.json' docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "echo 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> $PROJECT_DIR/cell_filtering/14490/discarded_cols.json" ## writing file $PROJECT_DIR/cell_filtering/14490/manually_discarded_cols.json echo '-> writing file $PROJECT_DIR/cell_filtering/14490/manually_discarded_cols.json' docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "echo '{"manually_discarded_cols":[]}' > $PROJECT_DIR/cell_filtering/14490/manually_discarded_cols.json" ## Running Cell filtering [14490] [Cell filtering #1 qc_plots] (depth:1000 detected_genes:100 protein_coding_content:80 mito_content:20 ribo_content:20 nber_manually_discarded_cols:0 input_matrix:parsing) echo '-> Running Cell filtering [14490] [Cell filtering #1 qc_plots] (depth:1000 detected_genes:100 protein_coding_content:80 mito_content:20 ribo_content:20 nber_manually_discarded_cols:0 input_matrix:parsing)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_14490 --net=host -e HOST_USER_ID=$(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 FilterCols -loom /data/asap2/users/1/ak9s4r/parsing/output.loom -o /data/asap2/users/1/ak9s4r/cell_filtering/14490 -col_indexes_file /data/asap2/users/1/ak9s4r/cell_filtering/14490/discarded_cols.json 1> /data/asap2/users/1/ak9s4r/cell_filtering/14490/exec.out 2> /data/asap2/users/1/ak9s4r/cell_filtering/14490/exec.err'" ## ---------------------------------------------------------------- ## Run 14503 Gene filtering (Gene filtering #1 hvg_scanpy) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/gene_filtering/14503/" ## Running Gene filtering [14503] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:None is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3) echo '-> Running Gene filtering [14503] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:None is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_14503 --net=host -e HOST_USER_ID=$(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 'python3 hvg_scanpy_opti.py /data/asap2/users/1/ak9s4r/cell_filtering/14490/output.loom /matrix /data/asap2/users/1/ak9s4r/gene_filtering/14503 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/ak9s4r/gene_filtering/14503/exec.out 2> /data/asap2/users/1/ak9s4r/gene_filtering/14503/exec.err'" ## ---------------------------------------------------------------- ## Run 14507 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 $PROJECT_DIR/normalization/14507/" ## Running Normalization [14507] [Normalization #1 asap_seurat] (input_matrix:cell_filtering #1 scale_factor:10000) echo '-> Running Normalization [14507] [Normalization #1 asap_seurat] (input_matrix:cell_filtering #1 scale_factor:10000)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_14507 --net=host -e HOST_USER_ID=$(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/ak9s4r/cell_filtering/14490/output.loom -o /data/asap2/users/1/ak9s4r/normalization/14507/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000 1> /data/asap2/users/1/ak9s4r/normalization/14507/exec.out 2> /data/asap2/users/1/ak9s4r/normalization/14507/exec.err'" ## ---------------------------------------------------------------- ## Run 14508 Normalization (Normalization #2 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 $PROJECT_DIR/normalization/14508/" ## Running Normalization [14508] [Normalization #2 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000) echo '-> Running Normalization [14508] [Normalization #2 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_14508 --net=host -e HOST_USER_ID=$(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/ak9s4r/gene_filtering/14503/output.loom -o /data/asap2/users/1/ak9s4r/normalization/14508/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000 1> /data/asap2/users/1/ak9s4r/normalization/14508/exec.out 2> /data/asap2/users/1/ak9s4r/normalization/14508/exec.err'" ## ---------------------------------------------------------------- ## Run 14513 Scaling (Scaling #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 $PROJECT_DIR/scaling/14513/" ## Running Scaling [14513] [Scaling #1 asap_seurat] (input_matrix:normalization #2 do_scale:true do_center:true scale_max:10) echo '-> Running Scaling [14513] [Scaling #1 asap_seurat] (input_matrix:normalization #2 do_scale:true do_center:true scale_max:10)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_14513 --net=host -e HOST_USER_ID=$(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 Scaling -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -o /data/asap2/users/1/ak9s4r/scaling/14513/output.json -iAnnot /layers/norm_2_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10 1> /data/asap2/users/1/ak9s4r/scaling/14513/exec.out 2> /data/asap2/users/1/ak9s4r/scaling/14513/exec.err'" ## ---------------------------------------------------------------- ## Run 14514 Dimension reduction (Dimension reduction #1 inc_pca) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/14514/" ## Running Dimension reduction [14514] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1 nber_dims:50) echo '-> Running Dimension reduction [14514] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1 nber_dims:50)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_14514 --net=host -e HOST_USER_ID=$(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 'python3 pca_scanpy_opti.py /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/ak9s4r/dim_reduction/14514/output.json 50 10000 20 1> /data/asap2/users/1/ak9s4r/dim_reduction/14514/exec.out 2> /data/asap2/users/1/ak9s4r/dim_reduction/14514/exec.err'" ## ---------------------------------------------------------------- ## Run 14861 Dimension reduction (Dimension reduction #2 umap) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/14861/" ## Running Dimension reduction [14861] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.1 n_neighbors:30 metric:correlation) echo '-> Running Dimension reduction [14861] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.1 n_neighbors:30 metric:correlation)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_14861 --net=host -e HOST_USER_ID=$(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 'Rscript --vanilla dimension_reduction.R /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom /data/asap2/users/1/ak9s4r/dim_reduction/14861 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_2_umap_2D 2 0.1 30 correlation 1> /data/asap2/users/1/ak9s4r/dim_reduction/14861/exec.out 2> /data/asap2/users/1/ak9s4r/dim_reduction/14861/exec.err'" ## ---------------------------------------------------------------- ## Run 15272 Clustering (Clustering #2 kmeans) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/clustering/15272/" ## Running Clustering [15272] [Clustering #2 kmeans] (input_matrix:dim_reduction #1 nb_clust:20 algorithm:Hartigan-Wong) echo '-> Running Clustering [15272] [Clustering #2 kmeans] (input_matrix:dim_reduction #1 nb_clust:20 algorithm:Hartigan-Wong)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_15272 --net=host -e HOST_USER_ID=$(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 'Rscript --vanilla clustering.R /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom /data/asap2/users/1/ak9s4r/clustering/15272 kmeans /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_2_kmeans 20 Hartigan-Wong 1> /data/asap2/users/1/ak9s4r/clustering/15272/exec.out 2> /data/asap2/users/1/ak9s4r/clustering/15272/exec.err'" ## ---------------------------------------------------------------- ## Run 16139 Clustering (Clustering #3 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 $PROJECT_DIR/clustering/16139/" ## Running Clustering [16139] [Clustering #3 seurat] (input_matrix:dim_reduction #1 k:100 resolution:0.5 algorithm:louvain graph_type:nn) echo '-> Running Clustering [16139] [Clustering #3 seurat] (input_matrix:dim_reduction #1 k:100 resolution:0.5 algorithm:louvain graph_type:nn)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16139 --net=host -e HOST_USER_ID=$(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 'Rscript --vanilla clustering.R /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom /data/asap2/users/1/ak9s4r/clustering/16139 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_3_seurat 100 0.5 louvain nn 1> /data/asap2/users/1/ak9s4r/clustering/16139/exec.out 2> /data/asap2/users/1/ak9s4r/clustering/16139/exec.err'" ## ---------------------------------------------------------------- ## Run 16672 Differential expression (Differential expression #1 wilcox_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 $PROJECT_DIR/de/16672/" ## Running Differential expression [16672] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #2 groups:clustering #3 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [16672] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #2 groups:clustering #3 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16672 --net=host -e HOST_USER_ID=$(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 'Rscript --vanilla de.R /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom /data/asap2/users/1/ak9s4r/de/16672 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_1_wilcox-seurat null /col_attrs/_clust_3_seurat 9 null false 0.1 null 1.3 null 1> /data/asap2/users/1/ak9s4r/de/16672/exec.out 2> /data/asap2/users/1/ak9s4r/de/16672/exec.err'" ## ---------------------------------------------------------------- ## Run 16681 Differential expression (Differential expression #10 wilcox_asap) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/16681/" ## Running Differential expression [16681] [Differential expression #10 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [16681] [Differential expression #10 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16681 --net=host -e HOST_USER_ID=$(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 DifferentialExpression -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -o /data/asap2/users/1/ak9s4r/de/16681 -m wilcox-asap -iAnnot /layers/norm_2_asap_seurat -oAnnot /row_attrs/_de_10_wilcox-asap -gAnnot /col_attrs/_clust_3_seurat -g1 9 -g2 null 1> /data/asap2/users/1/ak9s4r/de/16681/exec.out 2> /data/asap2/users/1/ak9s4r/de/16681/exec.err'" ## ---------------------------------------------------------------- ## Run 16731 Differential expression (Differential expression #11 wilcox_asap) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/16731/" ## Running Differential expression [16731] [Differential expression #11 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [16731] [Differential expression #11 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16731 --net=host -e HOST_USER_ID=$(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 DifferentialExpression -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -o /data/asap2/users/1/ak9s4r/de/16731 -m wilcox-asap -iAnnot /layers/norm_2_asap_seurat -oAnnot /row_attrs/_de_11_wilcox-asap -gAnnot /col_attrs/_clust_3_seurat -g1 14 -g2 null 1> /data/asap2/users/1/ak9s4r/de/16731/exec.out 2> /data/asap2/users/1/ak9s4r/de/16731/exec.err'" ## ---------------------------------------------------------------- ## Run 16732 Differential expression (Differential expression #12 wilcox_asap) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/16732/" ## Running Differential expression [16732] [Differential expression #12 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [16732] [Differential expression #12 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16732 --net=host -e HOST_USER_ID=$(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 DifferentialExpression -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -o /data/asap2/users/1/ak9s4r/de/16732 -m wilcox-asap -iAnnot /layers/norm_2_asap_seurat -oAnnot /row_attrs/_de_12_wilcox-asap -gAnnot /col_attrs/_clust_3_seurat -g1 15 -g2 null 1> /data/asap2/users/1/ak9s4r/de/16732/exec.out 2> /data/asap2/users/1/ak9s4r/de/16732/exec.err'" ## ---------------------------------------------------------------- ## Run 16733 Differential expression (Differential expression #13 wilcox_asap) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/16733/" ## Running Differential expression [16733] [Differential expression #13 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:17 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [16733] [Differential expression #13 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:17 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16733 --net=host -e HOST_USER_ID=$(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 DifferentialExpression -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -o /data/asap2/users/1/ak9s4r/de/16733 -m wilcox-asap -iAnnot /layers/norm_2_asap_seurat -oAnnot /row_attrs/_de_13_wilcox-asap -gAnnot /col_attrs/_clust_3_seurat -g1 17 -g2 null 1> /data/asap2/users/1/ak9s4r/de/16733/exec.out 2> /data/asap2/users/1/ak9s4r/de/16733/exec.err'" ## ---------------------------------------------------------------- ## Run 16734 Differential expression (Differential expression #14 wilcox_asap) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/16734/" ## Running Differential expression [16734] [Differential expression #14 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:18 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [16734] [Differential expression #14 wilcox_asap] (input_matrix:normalization #2 groups:clustering #3 group_ref:18 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16734 --net=host -e HOST_USER_ID=$(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 DifferentialExpression -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -o /data/asap2/users/1/ak9s4r/de/16734 -m wilcox-asap -iAnnot /layers/norm_2_asap_seurat -oAnnot /row_attrs/_de_14_wilcox-asap -gAnnot /col_attrs/_clust_3_seurat -g1 18 -g2 null 1> /data/asap2/users/1/ak9s4r/de/16734/exec.out 2> /data/asap2/users/1/ak9s4r/de/16734/exec.err'" ## ---------------------------------------------------------------- ## Run 16845 Gene Enrichment (Gene Enrichment #1 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16845/" ## Running Gene Enrichment [16845] [Gene Enrichment #1 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16845] [Gene Enrichment #1 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16845 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16734_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16845/output.json -max 500 -min 15 -adj fdr -geneset 2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16845/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16845/exec.err'" ## ---------------------------------------------------------------- ## Run 16846 Gene Enrichment (Gene Enrichment #2 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16846/" ## Running Gene Enrichment [16846] [Gene Enrichment #2 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16846] [Gene Enrichment #2 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16846 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16733_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16846/output.json -max 500 -min 15 -adj fdr -geneset 2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16846/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16846/exec.err'" ## ---------------------------------------------------------------- ## Run 16847 Gene Enrichment (Gene Enrichment #3 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16847/" ## Running Gene Enrichment [16847] [Gene Enrichment #3 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16847] [Gene Enrichment #3 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16847 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16732_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16847/output.json -max 500 -min 15 -adj fdr -geneset 2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16847/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16847/exec.err'" ## ---------------------------------------------------------------- ## Run 16848 Gene Enrichment (Gene Enrichment #4 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16848/" ## Running Gene Enrichment [16848] [Gene Enrichment #4 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16848] [Gene Enrichment #4 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16848 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16731_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16848/output.json -max 500 -min 15 -adj fdr -geneset 2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16848/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16848/exec.err'" ## ---------------------------------------------------------------- ## Run 16849 Gene Enrichment (Gene Enrichment #5 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16849/" ## Running Gene Enrichment [16849] [Gene Enrichment #5 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16849] [Gene Enrichment #5 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16849 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16681_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16849/output.json -max 500 -min 15 -adj fdr -geneset 2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16849/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16849/exec.err'" ## ---------------------------------------------------------------- ## Run 16850 Gene Enrichment (Gene Enrichment #6 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16850/" ## Running Gene Enrichment [16850] [Gene Enrichment #6 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16850] [Gene Enrichment #6 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16850 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16672_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16850/output.json -max 500 -min 15 -adj fdr -geneset 2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16850/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16850/exec.err'" ## ---------------------------------------------------------------- ## Run 16851 Gene Enrichment (Gene Enrichment #7 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16851/" ## Running Gene Enrichment [16851] [Gene Enrichment #7 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16851] [Gene Enrichment #7 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16851 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16734_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16851/output.json -max 500 -min 15 -adj fdr -geneset 57 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16851/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16851/exec.err'" ## ---------------------------------------------------------------- ## Run 16852 Gene Enrichment (Gene Enrichment #8 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16852/" ## Running Gene Enrichment [16852] [Gene Enrichment #8 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16852] [Gene Enrichment #8 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16852 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16733_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16852/output.json -max 500 -min 15 -adj fdr -geneset 57 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16852/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16852/exec.err'" ## ---------------------------------------------------------------- ## Run 16853 Gene Enrichment (Gene Enrichment #9 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16853/" ## Running Gene Enrichment [16853] [Gene Enrichment #9 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16853] [Gene Enrichment #9 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16853 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16732_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16853/output.json -max 500 -min 15 -adj fdr -geneset 57 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16853/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16853/exec.err'" ## ---------------------------------------------------------------- ## Run 16854 Gene Enrichment (Gene Enrichment #10 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16854/" ## Running Gene Enrichment [16854] [Gene Enrichment #10 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16854] [Gene Enrichment #10 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16854 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16731_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16854/output.json -max 500 -min 15 -adj fdr -geneset 57 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16854/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16854/exec.err'" ## ---------------------------------------------------------------- ## Run 16855 Gene Enrichment (Gene Enrichment #11 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16855/" ## Running Gene Enrichment [16855] [Gene Enrichment #11 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16855] [Gene Enrichment #11 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16855 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16681_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16855/output.json -max 500 -min 15 -adj fdr -geneset 57 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16855/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16855/exec.err'" ## ---------------------------------------------------------------- ## Run 16856 Gene Enrichment (Gene Enrichment #12 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16856/" ## Running Gene Enrichment [16856] [Gene Enrichment #12 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16856] [Gene Enrichment #12 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16856 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16672_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16856/output.json -max 500 -min 15 -adj fdr -geneset 57 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16856/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16856/exec.err'" ## ---------------------------------------------------------------- ## Run 16857 Gene Enrichment (Gene Enrichment #13 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16857/" ## Running Gene Enrichment [16857] [Gene Enrichment #13 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16857] [Gene Enrichment #13 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16857 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16734_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16857/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16857/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16857/exec.err'" ## ---------------------------------------------------------------- ## Run 16858 Gene Enrichment (Gene Enrichment #14 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16858/" ## Running Gene Enrichment [16858] [Gene Enrichment #14 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16858] [Gene Enrichment #14 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16858 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16733_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16858/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16858/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16858/exec.err'" ## ---------------------------------------------------------------- ## Run 16859 Gene Enrichment (Gene Enrichment #15 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16859/" ## Running Gene Enrichment [16859] [Gene Enrichment #15 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16859] [Gene Enrichment #15 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16859 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16732_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16859/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16859/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16859/exec.err'" ## ---------------------------------------------------------------- ## Run 16860 Gene Enrichment (Gene Enrichment #16 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16860/" ## Running Gene Enrichment [16860] [Gene Enrichment #16 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16860] [Gene Enrichment #16 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16860 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16731_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16860/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16860/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16860/exec.err'" ## ---------------------------------------------------------------- ## Run 16861 Gene Enrichment (Gene Enrichment #17 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16861/" ## Running Gene Enrichment [16861] [Gene Enrichment #17 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16861] [Gene Enrichment #17 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16861 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16681_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16861/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16861/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16861/exec.err'" ## ---------------------------------------------------------------- ## Run 16862 Gene Enrichment (Gene Enrichment #18 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16862/" ## Running Gene Enrichment [16862] [Gene Enrichment #18 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16862] [Gene Enrichment #18 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16862 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16672_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16862/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16862/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16862/exec.err'" ## ---------------------------------------------------------------- ## Run 16863 Gene Enrichment (Gene Enrichment #19 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16863/" ## Running Gene Enrichment [16863] [Gene Enrichment #19 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16863] [Gene Enrichment #19 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16863 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16734_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16863/output.json -max 500 -min 15 -adj fdr -geneset 2091 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16863/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16863/exec.err'" ## ---------------------------------------------------------------- ## Run 16864 Gene Enrichment (Gene Enrichment #20 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16864/" ## Running Gene Enrichment [16864] [Gene Enrichment #20 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16864] [Gene Enrichment #20 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16864 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16733_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16864/output.json -max 500 -min 15 -adj fdr -geneset 2091 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16864/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16864/exec.err'" ## ---------------------------------------------------------------- ## Run 16865 Gene Enrichment (Gene Enrichment #21 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16865/" ## Running Gene Enrichment [16865] [Gene Enrichment #21 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16865] [Gene Enrichment #21 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16865 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16732_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16865/output.json -max 500 -min 15 -adj fdr -geneset 2091 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16865/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16865/exec.err'" ## ---------------------------------------------------------------- ## Run 16866 Gene Enrichment (Gene Enrichment #22 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16866/" ## Running Gene Enrichment [16866] [Gene Enrichment #22 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16866] [Gene Enrichment #22 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16866 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16731_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16866/output.json -max 500 -min 15 -adj fdr -geneset 2091 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16866/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16866/exec.err'" ## ---------------------------------------------------------------- ## Run 16867 Gene Enrichment (Gene Enrichment #23 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16867/" ## Running Gene Enrichment [16867] [Gene Enrichment #23 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16867] [Gene Enrichment #23 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16867 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16681_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16867/output.json -max 500 -min 15 -adj fdr -geneset 2091 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16867/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16867/exec.err'" ## ---------------------------------------------------------------- ## Run 16868 Gene Enrichment (Gene Enrichment #24 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/16868/" ## Running Gene Enrichment [16868] [Gene Enrichment #24 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [16868] [Gene Enrichment #24 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_16868 --net=host -e HOST_USER_ID=$(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 Enrichment -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -m fet -f /data/asap2/users/1/ak9s4r/tmp/1_16672_2_0.05_filtered_ids.json -o /data/asap2/users/1/ak9s4r/ge/16868/output.json -max 500 -min 15 -adj fdr -geneset 2091 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v5 1> /data/asap2/users/1/ak9s4r/ge/16868/exec.out 2> /data/asap2/users/1/ak9s4r/ge/16868/exec.err'" ## ---------------------------------------------------------------- ## Run 16884 Cell selection (Cell selection #1 cell_sel) ## ---------------------------------------------------------------- ## 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/cell_selection/16884/" ## Running Cell selection [16884] [Cell selection #1 cell_sel] () echo '-> Running Cell selection [16884] [Cell selection #1 cell_sel] ()' ## Command sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/ak9s4r/gene_filtering/14503/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_1 -f /data/asap2/users/1/ak9s4r/metadata/16884/list_cols.json '