## This script contains all commands executed in the PROJECT wkqvt9 and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run) echo '*******************Reproducing analysis of PROJECT wkqvt9 / ASAP1**********************' 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/wkqvt9 ## Pull Docker images (must run before any docker run in this script) docker pull fabdavid/asap_run:v4 ## Host LOOM staging directory (inside Docker volume) docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $LOOM_DIR; chmod 777 $LOOM_DIR" echo 'This project is PUBLIC => Nothing to do' ## Local PostgreSQL: create ASAP data database and load dump if missing if ! psql -lqt | cut -d \| -f 1 | grep -qw asap_data_v4; then echo 'Create database asap_data_v4'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v4'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v4; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v4.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v4'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v4.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v4; fi ## Project directory on the shared volume docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -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:v4 -c "mkdir -p $PROJECT_DIR/cell_selection/ && mkdir -p $PROJECT_DIR/dim_reduction/ && mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/scaling/ && mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/gene_filtering/ && mkdir -p $PROJECT_DIR/cell_filtering/ && mkdir -p $PROJECT_DIR/de/ && mkdir -p $PROJECT_DIR/ge/" ## 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:v4 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/wkqvt9/get_file?filename=parsing/output.loom'" ## Re-execute each recorded run (parsing step is skipped; LOOM is already in place) ## ---------------------------------------------------------------- ## Run 11617 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:v4 -c "mkdir -p $PROJECT_DIR/cell_filtering/11617/" ## writing file $PROJECT_DIR/cell_filtering/11617/discarded_cols.json echo '-> writing file $PROJECT_DIR/cell_filtering/11617/discarded_cols.json' docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "echo '{"discarded_cols":[163,132,215,115]}' > $PROJECT_DIR/cell_filtering/11617/discarded_cols.json" ## writing file $PROJECT_DIR/cell_filtering/11617/manually_discarded_cols.json echo '-> writing file $PROJECT_DIR/cell_filtering/11617/manually_discarded_cols.json' docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "echo '{"manually_discarded_cols":[]}' > $PROJECT_DIR/cell_filtering/11617/manually_discarded_cols.json" ## Running Cell filtering [11617] [Cell filtering #1 qc_plots] (depth:500 detected_genes:100 mito_content:0 protein_coding_content:70 ribo_content:25 nber_manually_discarded_cols:0 input_matrix:parsing) echo '-> Running Cell filtering [11617] [Cell filtering #1 qc_plots] (depth:500 detected_genes:100 mito_content:0 protein_coding_content:70 ribo_content:25 nber_manually_discarded_cols:0 input_matrix:parsing)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11617 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterCols -loom /data/asap2/users/1/wkqvt9/parsing/output.loom -o /data/asap2/users/1/wkqvt9/cell_filtering/11617 -col_indexes_file /data/asap2/users/1/wkqvt9/cell_filtering/11617/discarded_cols.json 1> /data/asap2/users/1/wkqvt9/cell_filtering/11617/exec.out 2> /data/asap2/users/1/wkqvt9/cell_filtering/11617/exec.err'" ## ---------------------------------------------------------------- ## Run 11618 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:v4 -c "mkdir -p $PROJECT_DIR/gene_filtering/11618/" ## Running Gene filtering [11618] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:None is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3) echo '-> Running Gene filtering [11618] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:None is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11618 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'python3 hvg_scanpy_opti.py /data/asap2/users/1/wkqvt9/cell_filtering/11617/output.loom /matrix /data/asap2/users/1/wkqvt9/gene_filtering/11618 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/wkqvt9/gene_filtering/11618/exec.out 2> /data/asap2/users/1/wkqvt9/gene_filtering/11618/exec.err'" ## ---------------------------------------------------------------- ## Run 11619 Gene filtering (Gene filtering #2 hvg) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/gene_filtering/11619/" ## Running Gene filtering [11619] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1 fdr:0.1 min_disp:0.5) echo '-> Running Gene filtering [11619] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1 fdr:0.1 min_disp:0.5)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11619 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla filtering.R /data/asap2/users/1/wkqvt9/cell_filtering/11617/output.loom /data/asap2/users/1/wkqvt9/gene_filtering/11619 hvg false 0.1 0.5 1> /data/asap2/users/1/wkqvt9/gene_filtering/11619/exec.out 2> /data/asap2/users/1/wkqvt9/gene_filtering/11619/exec.err'" ## ---------------------------------------------------------------- ## Run 11620 Gene filtering (Gene filtering #3 m3drop) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/gene_filtering/11620/" ## Running Gene filtering [11620] [Gene filtering #3 m3drop] (input_matrix:cell_filtering #1 fdr:0.05) echo '-> Running Gene filtering [11620] [Gene filtering #3 m3drop] (input_matrix:cell_filtering #1 fdr:0.05)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11620 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla filtering.R /data/asap2/users/1/wkqvt9/cell_filtering/11617/output.loom /data/asap2/users/1/wkqvt9/gene_filtering/11620 m3drop 0.05 1> /data/asap2/users/1/wkqvt9/gene_filtering/11620/exec.out 2> /data/asap2/users/1/wkqvt9/gene_filtering/11620/exec.err'" ## ---------------------------------------------------------------- ## Run 11621 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:v4 -c "mkdir -p $PROJECT_DIR/normalization/11621/" ## Running Normalization [11621] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000) echo '-> Running Normalization [11621] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11621 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -o /data/asap2/users/1/wkqvt9/normalization/11621/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000 1> /data/asap2/users/1/wkqvt9/normalization/11621/exec.out 2> /data/asap2/users/1/wkqvt9/normalization/11621/exec.err'" ## ---------------------------------------------------------------- ## Run 11622 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:v4 -c "mkdir -p $PROJECT_DIR/scaling/11622/" ## Running Scaling [11622] [Scaling #1 asap_seurat] (input_matrix:normalization #1 do_scale:true do_center:true scale_max:10) echo '-> Running Scaling [11622] [Scaling #1 asap_seurat] (input_matrix:normalization #1 do_scale:true do_center:true scale_max:10)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11622 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Scaling -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -o /data/asap2/users/1/wkqvt9/scaling/11622/output.json -iAnnot /layers/norm_1_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10 1> /data/asap2/users/1/wkqvt9/scaling/11622/exec.out 2> /data/asap2/users/1/wkqvt9/scaling/11622/exec.err'" ## ---------------------------------------------------------------- ## Run 11623 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:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/11623/" ## Running Dimension reduction [11623] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1 nber_dims:50) echo '-> Running Dimension reduction [11623] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1 nber_dims:50)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11623 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'python3 pca_scanpy_opti.py /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/wkqvt9/dim_reduction/11623/output.json 50 10000 20 1> /data/asap2/users/1/wkqvt9/dim_reduction/11623/exec.out 2> /data/asap2/users/1/wkqvt9/dim_reduction/11623/exec.err'" ## ---------------------------------------------------------------- ## Run 11624 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:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/11624/" ## Running Dimension reduction [11624] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.2 n_neighbors:30 metric:correlation) echo '-> Running Dimension reduction [11624] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.2 n_neighbors:30 metric:correlation)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11624 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla dimension_reduction.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/dim_reduction/11624 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_2_umap_2D 2 0.2 30 correlation 1> /data/asap2/users/1/wkqvt9/dim_reduction/11624/exec.out 2> /data/asap2/users/1/wkqvt9/dim_reduction/11624/exec.err'" ## ---------------------------------------------------------------- ## Run 11625 Dimension reduction (Dimension reduction #3 umap) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/11625/" ## Running Dimension reduction [11625] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.2 n_neighbors:30 metric:correlation) echo '-> Running Dimension reduction [11625] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.2 n_neighbors:30 metric:correlation)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11625 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla dimension_reduction.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/dim_reduction/11625 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_3_umap_3D 3 0.2 30 correlation 1> /data/asap2/users/1/wkqvt9/dim_reduction/11625/exec.out 2> /data/asap2/users/1/wkqvt9/dim_reduction/11625/exec.err'" ## ---------------------------------------------------------------- ## Run 11626 Dimension reduction (Dimension reduction #4 tsne) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/11626/" ## Running Dimension reduction [11626] [Dimension reduction #4 tsne] (input_matrix:dim_reduction #1 nber_dims:2 perplexity:30 theta:0.5) echo '-> Running Dimension reduction [11626] [Dimension reduction #4 tsne] (input_matrix:dim_reduction #1 nber_dims:2 perplexity:30 theta:0.5)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11626 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla dimension_reduction.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/dim_reduction/11626 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_4_tsne_2D 2 30 0.5 1> /data/asap2/users/1/wkqvt9/dim_reduction/11626/exec.out 2> /data/asap2/users/1/wkqvt9/dim_reduction/11626/exec.err'" ## ---------------------------------------------------------------- ## Run 11627 Dimension reduction (Dimension reduction #5 tsne) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/dim_reduction/11627/" ## Running Dimension reduction [11627] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 nber_dims:3 perplexity:30 theta:0.5) echo '-> Running Dimension reduction [11627] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 nber_dims:3 perplexity:30 theta:0.5)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11627 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla dimension_reduction.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/dim_reduction/11627 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_5_tsne_3D 3 30 0.5 1> /data/asap2/users/1/wkqvt9/dim_reduction/11627/exec.out 2> /data/asap2/users/1/wkqvt9/dim_reduction/11627/exec.err'" ## ---------------------------------------------------------------- ## Run 11628 Clustering (Clustering #1 seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/clustering/11628/" ## Running Clustering [11628] [Clustering #1 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.8 algorithm:louvain) echo '-> Running Clustering [11628] [Clustering #1 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.8 algorithm:louvain)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11628 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla clustering.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/clustering/11628 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 20 0.8 louvain 1> /data/asap2/users/1/wkqvt9/clustering/11628/exec.out 2> /data/asap2/users/1/wkqvt9/clustering/11628/exec.err'" ## ---------------------------------------------------------------- ## Run 11630 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:v4 -c "mkdir -p $PROJECT_DIR/de/11630/" ## Running Differential expression [11630] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11630] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11630 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11630 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_1_wilcox-seurat null /col_attrs/_clust_1_seurat 1 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11630/exec.out 2> /data/asap2/users/1/wkqvt9/de/11630/exec.err'" ## ---------------------------------------------------------------- ## Run 11631 Differential expression (Differential expression #2 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11631/" ## Running Differential expression [11631] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:2 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11631] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:2 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11631 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11631 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_2_wilcox-seurat null /col_attrs/_clust_1_seurat 2 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11631/exec.out 2> /data/asap2/users/1/wkqvt9/de/11631/exec.err'" ## ---------------------------------------------------------------- ## Run 11632 Differential expression (Differential expression #3 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11632/" ## Running Differential expression [11632] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:3 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11632] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:3 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11632 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11632 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_3_wilcox-seurat null /col_attrs/_clust_1_seurat 3 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11632/exec.out 2> /data/asap2/users/1/wkqvt9/de/11632/exec.err'" ## ---------------------------------------------------------------- ## Run 11633 Differential expression (Differential expression #4 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11633/" ## Running Differential expression [11633] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:4 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11633] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:4 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11633 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11633 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_4_wilcox-seurat null /col_attrs/_clust_1_seurat 4 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11633/exec.out 2> /data/asap2/users/1/wkqvt9/de/11633/exec.err'" ## ---------------------------------------------------------------- ## Run 11634 Differential expression (Differential expression #5 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11634/" ## Running Differential expression [11634] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:5 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11634] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:5 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11634 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11634 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_5_wilcox-seurat null /col_attrs/_clust_1_seurat 5 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11634/exec.out 2> /data/asap2/users/1/wkqvt9/de/11634/exec.err'" ## ---------------------------------------------------------------- ## Run 11635 Differential expression (Differential expression #6 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11635/" ## Running Differential expression [11635] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11635] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11635 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11635 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_6_wilcox-seurat null /col_attrs/_clust_1_seurat 6 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11635/exec.out 2> /data/asap2/users/1/wkqvt9/de/11635/exec.err'" ## ---------------------------------------------------------------- ## Run 11636 Differential expression (Differential expression #7 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11636/" ## Running Differential expression [11636] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:7 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11636] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:7 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11636 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11636 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_7_wilcox-seurat null /col_attrs/_clust_1_seurat 7 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11636/exec.out 2> /data/asap2/users/1/wkqvt9/de/11636/exec.err'" ## ---------------------------------------------------------------- ## Run 11637 Differential expression (Differential expression #8 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11637/" ## Running Differential expression [11637] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:8 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11637] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:8 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11637 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11637 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_8_wilcox-seurat null /col_attrs/_clust_1_seurat 8 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11637/exec.out 2> /data/asap2/users/1/wkqvt9/de/11637/exec.err'" ## ---------------------------------------------------------------- ## Run 11638 Differential expression (Differential expression #9 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11638/" ## Running Differential expression [11638] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11638] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11638 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11638 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_9_wilcox-seurat null /col_attrs/_clust_1_seurat 9 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11638/exec.out 2> /data/asap2/users/1/wkqvt9/de/11638/exec.err'" ## ---------------------------------------------------------------- ## Run 11639 Differential expression (Differential expression #10 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11639/" ## Running Differential expression [11639] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:10 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11639] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:10 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11639 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11639 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_10_wilcox-seurat null /col_attrs/_clust_1_seurat 10 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11639/exec.out 2> /data/asap2/users/1/wkqvt9/de/11639/exec.err'" ## ---------------------------------------------------------------- ## Run 11640 Differential expression (Differential expression #11 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11640/" ## Running Differential expression [11640] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:11 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11640] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:11 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11640 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11640 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_11_wilcox-seurat null /col_attrs/_clust_1_seurat 11 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11640/exec.out 2> /data/asap2/users/1/wkqvt9/de/11640/exec.err'" ## ---------------------------------------------------------------- ## Run 11641 Differential expression (Differential expression #12 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11641/" ## Running Differential expression [11641] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11641] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11641 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11641 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_12_wilcox-seurat null /col_attrs/_clust_1_seurat 12 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11641/exec.out 2> /data/asap2/users/1/wkqvt9/de/11641/exec.err'" ## ---------------------------------------------------------------- ## Run 11642 Differential expression (Differential expression #13 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11642/" ## Running Differential expression [11642] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:13 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11642] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:13 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11642 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11642 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_13_wilcox-seurat null /col_attrs/_clust_1_seurat 13 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11642/exec.out 2> /data/asap2/users/1/wkqvt9/de/11642/exec.err'" ## ---------------------------------------------------------------- ## Run 11643 Differential expression (Differential expression #14 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11643/" ## Running Differential expression [11643] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11643] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11643 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11643 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_14_wilcox-seurat null /col_attrs/_clust_1_seurat 14 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11643/exec.out 2> /data/asap2/users/1/wkqvt9/de/11643/exec.err'" ## ---------------------------------------------------------------- ## Run 11644 Differential expression (Differential expression #15 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11644/" ## Running Differential expression [11644] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11644] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11644 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11644 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_15_wilcox-seurat null /col_attrs/_clust_1_seurat 15 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11644/exec.out 2> /data/asap2/users/1/wkqvt9/de/11644/exec.err'" ## ---------------------------------------------------------------- ## Run 11645 Differential expression (Differential expression #16 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11645/" ## Running Differential expression [11645] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:16 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11645] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:16 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11645 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11645 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_16_wilcox-seurat null /col_attrs/_clust_1_seurat 16 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11645/exec.out 2> /data/asap2/users/1/wkqvt9/de/11645/exec.err'" ## ---------------------------------------------------------------- ## Run 11648 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:v4 -c "mkdir -p $PROJECT_DIR/normalization/11648/" ## Running Normalization [11648] [Normalization #2 asap_seurat] (input_matrix:cell_filtering #1 scale_factor:10000) echo '-> Running Normalization [11648] [Normalization #2 asap_seurat] (input_matrix:cell_filtering #1 scale_factor:10000)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11648 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/1/wkqvt9/cell_filtering/11617/output.loom -o /data/asap2/users/1/wkqvt9/normalization/11648/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000 1> /data/asap2/users/1/wkqvt9/normalization/11648/exec.out 2> /data/asap2/users/1/wkqvt9/normalization/11648/exec.err'" ## ---------------------------------------------------------------- ## Run 11668 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11668/" ## Running Gene Enrichment [11668] [Gene Enrichment #1 basic] (input_de:de #16 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11668] [Gene Enrichment #1 basic] (input_de:de #16 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11668 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11645_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11668/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11668/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11668/exec.err'" ## ---------------------------------------------------------------- ## Run 11669 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11669/" ## Running Gene Enrichment [11669] [Gene Enrichment #2 basic] (input_de:de #15 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11669] [Gene Enrichment #2 basic] (input_de:de #15 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11669 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11644_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11669/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11669/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11669/exec.err'" ## ---------------------------------------------------------------- ## Run 11670 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11670/" ## Running Gene Enrichment [11670] [Gene Enrichment #3 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11670] [Gene Enrichment #3 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11670 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11643_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11670/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11670/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11670/exec.err'" ## ---------------------------------------------------------------- ## Run 11671 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11671/" ## Running Gene Enrichment [11671] [Gene Enrichment #4 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11671] [Gene Enrichment #4 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11671 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11642_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11671/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11671/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11671/exec.err'" ## ---------------------------------------------------------------- ## Run 11672 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11672/" ## Running Gene Enrichment [11672] [Gene Enrichment #5 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11672] [Gene Enrichment #5 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11672 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11641_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11672/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11672/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11672/exec.err'" ## ---------------------------------------------------------------- ## Run 11673 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11673/" ## Running Gene Enrichment [11673] [Gene Enrichment #6 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11673] [Gene Enrichment #6 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11673 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11640_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11673/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11673/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11673/exec.err'" ## ---------------------------------------------------------------- ## Run 11674 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11674/" ## Running Gene Enrichment [11674] [Gene Enrichment #7 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11674] [Gene Enrichment #7 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11674 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11639_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11674/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11674/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11674/exec.err'" ## ---------------------------------------------------------------- ## Run 11675 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11675/" ## Running Gene Enrichment [11675] [Gene Enrichment #8 basic] (input_de:de #9 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11675] [Gene Enrichment #8 basic] (input_de:de #9 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11675 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11638_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11675/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11675/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11675/exec.err'" ## ---------------------------------------------------------------- ## Run 11676 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11676/" ## Running Gene Enrichment [11676] [Gene Enrichment #9 basic] (input_de:de #8 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11676] [Gene Enrichment #9 basic] (input_de:de #8 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11676 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11637_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11676/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11676/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11676/exec.err'" ## ---------------------------------------------------------------- ## Run 11677 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11677/" ## Running Gene Enrichment [11677] [Gene Enrichment #10 basic] (input_de:de #7 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11677] [Gene Enrichment #10 basic] (input_de:de #7 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11677 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11636_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11677/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11677/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11677/exec.err'" ## ---------------------------------------------------------------- ## Run 11678 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11678/" ## Running Gene Enrichment [11678] [Gene Enrichment #11 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11678] [Gene Enrichment #11 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11678 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11635_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11678/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11678/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11678/exec.err'" ## ---------------------------------------------------------------- ## Run 11679 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11679/" ## Running Gene Enrichment [11679] [Gene Enrichment #12 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11679] [Gene Enrichment #12 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11679 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11634_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11679/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11679/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11679/exec.err'" ## ---------------------------------------------------------------- ## Run 11680 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11680/" ## Running Gene Enrichment [11680] [Gene Enrichment #13 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11680] [Gene Enrichment #13 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11680 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11633_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11680/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11680/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11680/exec.err'" ## ---------------------------------------------------------------- ## Run 11681 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11681/" ## Running Gene Enrichment [11681] [Gene Enrichment #14 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11681] [Gene Enrichment #14 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11681 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11632_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11681/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11681/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11681/exec.err'" ## ---------------------------------------------------------------- ## Run 11682 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11682/" ## Running Gene Enrichment [11682] [Gene Enrichment #15 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11682] [Gene Enrichment #15 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11682 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11631_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11682/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11682/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11682/exec.err'" ## ---------------------------------------------------------------- ## Run 11683 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11683/" ## Running Gene Enrichment [11683] [Gene Enrichment #16 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11683] [Gene Enrichment #16 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11683 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11630_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11683/output.json -max 500 -min 15 -adj fdr -geneset 2371 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11683/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11683/exec.err'" ## ---------------------------------------------------------------- ## Run 11684 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11684/" ## Running Gene Enrichment [11684] [Gene Enrichment #17 basic] (input_de:de #16 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11684] [Gene Enrichment #17 basic] (input_de:de #16 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11684 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11645_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11684/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11684/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11684/exec.err'" ## ---------------------------------------------------------------- ## Run 11685 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11685/" ## Running Gene Enrichment [11685] [Gene Enrichment #18 basic] (input_de:de #15 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11685] [Gene Enrichment #18 basic] (input_de:de #15 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11685 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11644_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11685/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11685/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11685/exec.err'" ## ---------------------------------------------------------------- ## Run 11686 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11686/" ## Running Gene Enrichment [11686] [Gene Enrichment #19 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11686] [Gene Enrichment #19 basic] (input_de:de #14 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11686 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11643_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11686/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11686/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11686/exec.err'" ## ---------------------------------------------------------------- ## Run 11687 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11687/" ## Running Gene Enrichment [11687] [Gene Enrichment #20 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11687] [Gene Enrichment #20 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11687 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11642_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11687/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11687/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11687/exec.err'" ## ---------------------------------------------------------------- ## Run 11688 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11688/" ## Running Gene Enrichment [11688] [Gene Enrichment #21 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11688] [Gene Enrichment #21 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11688 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11641_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11688/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11688/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11688/exec.err'" ## ---------------------------------------------------------------- ## Run 11689 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11689/" ## Running Gene Enrichment [11689] [Gene Enrichment #22 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11689] [Gene Enrichment #22 basic] (input_de:de #11 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11689 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11640_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11689/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11689/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11689/exec.err'" ## ---------------------------------------------------------------- ## Run 11690 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11690/" ## Running Gene Enrichment [11690] [Gene Enrichment #23 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11690] [Gene Enrichment #23 basic] (input_de:de #10 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11690 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11639_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11690/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11690/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11690/exec.err'" ## ---------------------------------------------------------------- ## Run 11691 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:v4 -c "mkdir -p $PROJECT_DIR/ge/11691/" ## Running Gene Enrichment [11691] [Gene Enrichment #24 basic] (input_de:de #9 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11691] [Gene Enrichment #24 basic] (input_de:de #9 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11691 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11638_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11691/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11691/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11691/exec.err'" ## ---------------------------------------------------------------- ## Run 11692 Gene Enrichment (Gene Enrichment #25 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/11692/" ## Running Gene Enrichment [11692] [Gene Enrichment #25 basic] (input_de:de #8 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11692] [Gene Enrichment #25 basic] (input_de:de #8 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11692 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11637_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11692/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11692/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11692/exec.err'" ## ---------------------------------------------------------------- ## Run 11693 Gene Enrichment (Gene Enrichment #26 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/11693/" ## Running Gene Enrichment [11693] [Gene Enrichment #26 basic] (input_de:de #7 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11693] [Gene Enrichment #26 basic] (input_de:de #7 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11693 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11636_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11693/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11693/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11693/exec.err'" ## ---------------------------------------------------------------- ## Run 11694 Gene Enrichment (Gene Enrichment #27 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/11694/" ## Running Gene Enrichment [11694] [Gene Enrichment #27 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11694] [Gene Enrichment #27 basic] (input_de:de #6 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11694 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11635_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11694/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11694/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11694/exec.err'" ## ---------------------------------------------------------------- ## Run 11695 Gene Enrichment (Gene Enrichment #28 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/11695/" ## Running Gene Enrichment [11695] [Gene Enrichment #28 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11695] [Gene Enrichment #28 basic] (input_de:de #5 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11695 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11634_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11695/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11695/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11695/exec.err'" ## ---------------------------------------------------------------- ## Run 11696 Gene Enrichment (Gene Enrichment #29 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/11696/" ## Running Gene Enrichment [11696] [Gene Enrichment #29 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11696] [Gene Enrichment #29 basic] (input_de:de #4 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11696 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11633_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11696/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11696/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11696/exec.err'" ## ---------------------------------------------------------------- ## Run 11697 Gene Enrichment (Gene Enrichment #30 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/11697/" ## Running Gene Enrichment [11697] [Gene Enrichment #30 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11697] [Gene Enrichment #30 basic] (input_de:de #3 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11697 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11632_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11697/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11697/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11697/exec.err'" ## ---------------------------------------------------------------- ## Run 11698 Gene Enrichment (Gene Enrichment #31 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/11698/" ## Running Gene Enrichment [11698] [Gene Enrichment #31 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11698] [Gene Enrichment #31 basic] (input_de:de #2 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11698 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11631_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11698/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11698/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11698/exec.err'" ## ---------------------------------------------------------------- ## Run 11699 Gene Enrichment (Gene Enrichment #32 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/ge/11699/" ## Running Gene Enrichment [11699] [Gene Enrichment #32 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [11699] [Gene Enrichment #32 basic] (input_de:de #1 fdr_cutoff:0.05 fc_cutoff:2 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11699 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -m fet -f /data/asap2/users/1/wkqvt9/tmp/1_11630_2_0.05_filtered_ids.json -o /data/asap2/users/1/wkqvt9/ge/11699/output.json -max 500 -min 15 -adj fdr -geneset 671 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v4 1> /data/asap2/users/1/wkqvt9/ge/11699/exec.out 2> /data/asap2/users/1/wkqvt9/ge/11699/exec.err'" ## ---------------------------------------------------------------- ## Run 11700 Clustering (Clustering #2 seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/clustering/11700/" ## Running Clustering [11700] [Clustering #2 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.5 algorithm:leiden) echo '-> Running Clustering [11700] [Clustering #2 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.5 algorithm:leiden)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11700 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla clustering.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/clustering/11700 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_2_seurat 20 0.5 leiden 1> /data/asap2/users/1/wkqvt9/clustering/11700/exec.out 2> /data/asap2/users/1/wkqvt9/clustering/11700/exec.err'" ## ---------------------------------------------------------------- ## Run 11701 Clustering (Clustering #3 seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/clustering/11701/" ## Running Clustering [11701] [Clustering #3 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.9 algorithm:leiden) echo '-> Running Clustering [11701] [Clustering #3 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.9 algorithm:leiden)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11701 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla clustering.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/clustering/11701 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_3_seurat 20 0.9 leiden 1> /data/asap2/users/1/wkqvt9/clustering/11701/exec.out 2> /data/asap2/users/1/wkqvt9/clustering/11701/exec.err'" ## ---------------------------------------------------------------- ## Run 11702 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:v4 -c "mkdir -p $PROJECT_DIR/cell_selection/11702/" ## Running Cell selection [11702] [Cell selection #1 cell_sel] () echo '-> Running Cell selection [11702] [Cell selection #1 cell_sel] ()' ## Command sh -c 'java -jar lib/ASAP.jar -T CreateCellSelection -loom /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom -meta /col_attrs/_dr_2_umap_2D.sel_1 -f /data/asap2/users/1/wkqvt9/metadata/11702/list_cols.json ' ## ---------------------------------------------------------------- ## Run 11703 Differential expression (Differential expression #17 wilcox-seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "mkdir -p $PROJECT_DIR/de/11703/" ## Running Differential expression [11703] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #1 groups:cell_selection #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [11703] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #1 groups:cell_selection #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11703 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/1/wkqvt9/gene_filtering/11618/output.loom /data/asap2/users/1/wkqvt9/de/11703 wilcox-seurat /layers/norm_1_asap_seurat /row_attrs/_de_17_wilcox-seurat null /col_attrs/_dr_2_umap_2D.sel_1 1 null false 0.1 null 1.3 null 1> /data/asap2/users/1/wkqvt9/de/11703/exec.out 2> /data/asap2/users/1/wkqvt9/de/11703/exec.err'"