## This script contains all commands executed in the PROJECT xj31a6 and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run) echo '*******************Reproducing analysis of PROJECT xj31a6 / ASAP3**********************' 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/xj31a6 ## 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/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/cell_filtering/ && 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:v4 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/xj31a6/get_file?filename=parsing/output.loom'" ## Re-execute each recorded run (parsing step is skipped; LOOM is already in place) ## ---------------------------------------------------------------- ## Run 11098 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/11098/" ## writing file $PROJECT_DIR/cell_filtering/11098/discarded_cols.json echo '-> writing file $PROJECT_DIR/cell_filtering/11098/discarded_cols.json' docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v4 -c "echo 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","41263","41273","41282","41291","41306","41308","41315","41316","41317","41332","41344","41345"]}' > $PROJECT_DIR/cell_filtering/11098/discarded_cols.json" ## writing file $PROJECT_DIR/cell_filtering/11098/manually_discarded_cols.json echo '-> writing file $PROJECT_DIR/cell_filtering/11098/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":[]}' > $PROJECT_DIR/cell_filtering/11098/manually_discarded_cols.json" ## Running Cell filtering [11098] [Cell filtering #1 qc_plots] (depth:100 detected_genes:100 protein_coding_content:40 mito_content:40 ribo_content:40 nber_manually_discarded_cols:0 input_matrix:parsing) echo '-> Running Cell filtering [11098] [Cell filtering #1 qc_plots] (depth:100 detected_genes:100 protein_coding_content:40 mito_content:40 ribo_content:40 nber_manually_discarded_cols:0 input_matrix:parsing)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11098 --net=host -e HOST_USER_ID=$(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/xj31a6/parsing/output.loom -o /data/asap2/users/1/xj31a6/cell_filtering/11098 -col_indexes_file /data/asap2/users/1/xj31a6/cell_filtering/11098/discarded_cols.json 1> /data/asap2/users/1/xj31a6/cell_filtering/11098/exec.out 2> /data/asap2/users/1/xj31a6/cell_filtering/11098/exec.err'" ## ---------------------------------------------------------------- ## Run 11121 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 $PROJECT_DIR/gene_filtering/11121/" ## Running Gene filtering [11121] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:None is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3) echo '-> Running Gene filtering [11121] [Gene filtering #1 hvg_scanpy] (input_matrix:cell_filtering #1 n_bins:20 n_top_genes:None is_logged:false min_disp:0.5 max_disp:Inf min_mean:0.0125 max_mean:3)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11121 --net=host -e HOST_USER_ID=$(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/xj31a6/cell_filtering/11098/output.loom /matrix /data/asap2/users/1/xj31a6/gene_filtering/11121 0.5 0.0125 3 Inf 20 None false 1> /data/asap2/users/1/xj31a6/gene_filtering/11121/exec.out 2> /data/asap2/users/1/xj31a6/gene_filtering/11121/exec.err'" ## ---------------------------------------------------------------- ## Run 11122 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 $PROJECT_DIR/gene_filtering/11122/" ## Running Gene filtering [11122] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1 fdr:0.1 min_disp:0.5) echo '-> Running Gene filtering [11122] [Gene filtering #2 hvg] (input_matrix:cell_filtering #1 fdr:0.1 min_disp:0.5)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11122 --net=host -e HOST_USER_ID=$(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/xj31a6/cell_filtering/11098/output.loom /data/asap2/users/1/xj31a6/gene_filtering/11122 hvg false 0.1 0.5 1> /data/asap2/users/1/xj31a6/gene_filtering/11122/exec.out 2> /data/asap2/users/1/xj31a6/gene_filtering/11122/exec.err'" ## ---------------------------------------------------------------- ## Run 11123 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 $PROJECT_DIR/gene_filtering/11123/" ## Running Gene filtering [11123] [Gene filtering #3 m3drop] (input_matrix:cell_filtering #1 fdr:0.05) echo '-> Running Gene filtering [11123] [Gene filtering #3 m3drop] (input_matrix:cell_filtering #1 fdr:0.05)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_11123 --net=host -e HOST_USER_ID=$(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/xj31a6/cell_filtering/11098/output.loom /data/asap2/users/1/xj31a6/gene_filtering/11123 m3drop 0.05 1> /data/asap2/users/1/xj31a6/gene_filtering/11123/exec.out 2> /data/asap2/users/1/xj31a6/gene_filtering/11123/exec.err'" ## ---------------------------------------------------------------- ## Run 13100 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 $PROJECT_DIR/normalization/13100/" ## Running Normalization [13100] [Normalization #1 asap_seurat] (input_matrix:cell_filtering #1 scale_factor:10000) echo '-> Running Normalization [13100] [Normalization #1 asap_seurat] (input_matrix:cell_filtering #1 scale_factor:10000)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13100 --net=host -e HOST_USER_ID=$(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/xj31a6/cell_filtering/11098/output.loom -o /data/asap2/users/1/xj31a6/normalization/13100/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000 1> /data/asap2/users/1/xj31a6/normalization/13100/exec.out 2> /data/asap2/users/1/xj31a6/normalization/13100/exec.err'" ## ---------------------------------------------------------------- ## Run 13101 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 $PROJECT_DIR/normalization/13101/" ## Running Normalization [13101] [Normalization #2 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000) echo '-> Running Normalization [13101] [Normalization #2 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13101 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom -o /data/asap2/users/1/xj31a6/normalization/13101/output.json -oAnnot /layers/norm_2_asap_seurat -scaleFactor 10000 1> /data/asap2/users/1/xj31a6/normalization/13101/exec.out 2> /data/asap2/users/1/xj31a6/normalization/13101/exec.err'" ## ---------------------------------------------------------------- ## Run 13104 Gene filtering (Gene filtering #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 $PROJECT_DIR/gene_filtering/13104/" ## Running Gene filtering [13104] [Gene filtering #4 basic] (input_matrix:cell_filtering #1) echo '-> Running Gene filtering [13104] [Gene filtering #4 basic] (input_matrix:cell_filtering #1)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13104 --net=host -e HOST_USER_ID=$(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 FilterRows -loom /data/asap2/users/1/xj31a6/cell_filtering/11098/output.loom -o /data/asap2/users/1/xj31a6/gene_filtering/13104 -m basic 1> /data/asap2/users/1/xj31a6/gene_filtering/13104/exec.out 2> /data/asap2/users/1/xj31a6/gene_filtering/13104/exec.err'" ## ---------------------------------------------------------------- ## Run 13105 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 $PROJECT_DIR/scaling/13105/" ## Running Scaling [13105] [Scaling #1 asap_seurat] (input_matrix:normalization #2 do_scale:true do_center:true scale_max:10) echo '-> Running Scaling [13105] [Scaling #1 asap_seurat] (input_matrix:normalization #2 do_scale:true do_center:true scale_max:10)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13105 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom -o /data/asap2/users/1/xj31a6/scaling/13105/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/xj31a6/scaling/13105/exec.out 2> /data/asap2/users/1/xj31a6/scaling/13105/exec.err'" ## ---------------------------------------------------------------- ## Run 13110 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 $PROJECT_DIR/dim_reduction/13110/" ## Running Dimension reduction [13110] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1 nber_dims:50) echo '-> Running Dimension reduction [13110] [Dimension reduction #1 inc_pca] (input_matrix:scaling #1 nber_dims:50)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13110 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /layers/scaling_1_asap_seurat /col_attrs/_dr_1_inc_pca_50D /data/asap2/users/1/xj31a6/dim_reduction/13110/output.json 50 10000 20 1> /data/asap2/users/1/xj31a6/dim_reduction/13110/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13110/exec.err'" ## ---------------------------------------------------------------- ## Run 13116 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 $PROJECT_DIR/clustering/13116/" ## Running Clustering [13116] [Clustering #1 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.8 algorithm:louvain) echo '-> Running Clustering [13116] [Clustering #1 seurat] (input_matrix:dim_reduction #1 k:20 resolution:0.8 algorithm:louvain)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13116 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/clustering/13116 seurat /col_attrs/_dr_1_inc_pca_50D /col_attrs/_clust_1_seurat 20 0.8 louvain 1> /data/asap2/users/1/xj31a6/clustering/13116/exec.out 2> /data/asap2/users/1/xj31a6/clustering/13116/exec.err'" ## ---------------------------------------------------------------- ## Run 13133 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 $PROJECT_DIR/dim_reduction/13133/" ## Running Dimension reduction [13133] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.05 n_neighbors:30 metric:correlation) echo '-> Running Dimension reduction [13133] [Dimension reduction #2 umap] (input_matrix:dim_reduction #1 nber_dims:2 min_dist:0.05 n_neighbors:30 metric:correlation)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13133 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/dim_reduction/13133 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_2_umap_2D 2 0.05 30 correlation 1> /data/asap2/users/1/xj31a6/dim_reduction/13133/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13133/exec.err'" ## ---------------------------------------------------------------- ## Run 13134 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 $PROJECT_DIR/dim_reduction/13134/" ## Running Dimension reduction [13134] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.05 n_neighbors:30 metric:correlation) echo '-> Running Dimension reduction [13134] [Dimension reduction #3 umap] (input_matrix:dim_reduction #1 nber_dims:3 min_dist:0.05 n_neighbors:30 metric:correlation)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13134 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/dim_reduction/13134 umap /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_3_umap_3D 3 0.05 30 correlation 1> /data/asap2/users/1/xj31a6/dim_reduction/13134/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13134/exec.err'" ## ---------------------------------------------------------------- ## Run 13136 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 $PROJECT_DIR/dim_reduction/13136/" ## Running Dimension reduction [13136] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 nber_dims:3 perplexity:200 theta:0) echo '-> Running Dimension reduction [13136] [Dimension reduction #5 tsne] (input_matrix:dim_reduction #1 nber_dims:3 perplexity:200 theta:0)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13136 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/dim_reduction/13136 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_5_tsne_3D 3 200 0 1> /data/asap2/users/1/xj31a6/dim_reduction/13136/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13136/exec.err'" ## ---------------------------------------------------------------- ## Run 13296 Dimension reduction (Dimension reduction #6 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 $PROJECT_DIR/dim_reduction/13296/" ## Running Dimension reduction [13296] [Dimension reduction #6 tsne] (input_matrix:dim_reduction #1 nber_dims:2 perplexity:200 theta:0) echo '-> Running Dimension reduction [13296] [Dimension reduction #6 tsne] (input_matrix:dim_reduction #1 nber_dims:2 perplexity:200 theta:0)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13296 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/dim_reduction/13296 tsne /col_attrs/_dr_1_inc_pca_50D /col_attrs/_dr_6_tsne_2D 2 200 0 1> /data/asap2/users/1/xj31a6/dim_reduction/13296/exec.out 2> /data/asap2/users/1/xj31a6/dim_reduction/13296/exec.err'" ## ---------------------------------------------------------------- ## Run 13563 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 $PROJECT_DIR/de/13563/" ## Running Differential expression [13563] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13563] [Differential expression #1 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13563 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13563 wilcox-seurat /layers/norm_2_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/xj31a6/de/13563/exec.out 2> /data/asap2/users/1/xj31a6/de/13563/exec.err'" ## ---------------------------------------------------------------- ## Run 13564 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 $PROJECT_DIR/de/13564/" ## Running Differential expression [13564] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:2 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13564] [Differential expression #2 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:2 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13564 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13564 wilcox-seurat /layers/norm_2_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/xj31a6/de/13564/exec.out 2> /data/asap2/users/1/xj31a6/de/13564/exec.err'" ## ---------------------------------------------------------------- ## Run 13565 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 $PROJECT_DIR/de/13565/" ## Running Differential expression [13565] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:3 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13565] [Differential expression #3 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:3 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13565 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13565 wilcox-seurat /layers/norm_2_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/xj31a6/de/13565/exec.out 2> /data/asap2/users/1/xj31a6/de/13565/exec.err'" ## ---------------------------------------------------------------- ## Run 13566 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 $PROJECT_DIR/de/13566/" ## Running Differential expression [13566] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:4 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13566] [Differential expression #4 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:4 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13566 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13566 wilcox-seurat /layers/norm_2_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/xj31a6/de/13566/exec.out 2> /data/asap2/users/1/xj31a6/de/13566/exec.err'" ## ---------------------------------------------------------------- ## Run 13567 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 $PROJECT_DIR/de/13567/" ## Running Differential expression [13567] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:5 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13567] [Differential expression #5 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:5 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13567 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13567 wilcox-seurat /layers/norm_2_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/xj31a6/de/13567/exec.out 2> /data/asap2/users/1/xj31a6/de/13567/exec.err'" ## ---------------------------------------------------------------- ## Run 13568 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 $PROJECT_DIR/de/13568/" ## Running Differential expression [13568] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13568] [Differential expression #6 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13568 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13568 wilcox-seurat /layers/norm_2_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/xj31a6/de/13568/exec.out 2> /data/asap2/users/1/xj31a6/de/13568/exec.err'" ## ---------------------------------------------------------------- ## Run 13569 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 $PROJECT_DIR/de/13569/" ## Running Differential expression [13569] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:7 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13569] [Differential expression #7 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:7 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13569 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13569 wilcox-seurat /layers/norm_2_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/xj31a6/de/13569/exec.out 2> /data/asap2/users/1/xj31a6/de/13569/exec.err'" ## ---------------------------------------------------------------- ## Run 13570 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 $PROJECT_DIR/de/13570/" ## Running Differential expression [13570] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:8 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13570] [Differential expression #8 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:8 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13570 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13570 wilcox-seurat /layers/norm_2_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/xj31a6/de/13570/exec.out 2> /data/asap2/users/1/xj31a6/de/13570/exec.err'" ## ---------------------------------------------------------------- ## Run 13571 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 $PROJECT_DIR/de/13571/" ## Running Differential expression [13571] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13571] [Differential expression #9 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13571 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13571 wilcox-seurat /layers/norm_2_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/xj31a6/de/13571/exec.out 2> /data/asap2/users/1/xj31a6/de/13571/exec.err'" ## ---------------------------------------------------------------- ## Run 13572 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 $PROJECT_DIR/de/13572/" ## Running Differential expression [13572] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:10 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13572] [Differential expression #10 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:10 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13572 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13572 wilcox-seurat /layers/norm_2_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/xj31a6/de/13572/exec.out 2> /data/asap2/users/1/xj31a6/de/13572/exec.err'" ## ---------------------------------------------------------------- ## Run 13573 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 $PROJECT_DIR/de/13573/" ## Running Differential expression [13573] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:11 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13573] [Differential expression #11 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:11 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13573 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13573 wilcox-seurat /layers/norm_2_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/xj31a6/de/13573/exec.out 2> /data/asap2/users/1/xj31a6/de/13573/exec.err'" ## ---------------------------------------------------------------- ## Run 13574 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 $PROJECT_DIR/de/13574/" ## Running Differential expression [13574] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13574] [Differential expression #12 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13574 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13574 wilcox-seurat /layers/norm_2_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/xj31a6/de/13574/exec.out 2> /data/asap2/users/1/xj31a6/de/13574/exec.err'" ## ---------------------------------------------------------------- ## Run 13575 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 $PROJECT_DIR/de/13575/" ## Running Differential expression [13575] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:13 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13575] [Differential expression #13 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:13 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13575 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13575 wilcox-seurat /layers/norm_2_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/xj31a6/de/13575/exec.out 2> /data/asap2/users/1/xj31a6/de/13575/exec.err'" ## ---------------------------------------------------------------- ## Run 13576 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 $PROJECT_DIR/de/13576/" ## Running Differential expression [13576] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13576] [Differential expression #14 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13576 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13576 wilcox-seurat /layers/norm_2_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/xj31a6/de/13576/exec.out 2> /data/asap2/users/1/xj31a6/de/13576/exec.err'" ## ---------------------------------------------------------------- ## Run 13577 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 $PROJECT_DIR/de/13577/" ## Running Differential expression [13577] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13577] [Differential expression #15 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13577 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13577 wilcox-seurat /layers/norm_2_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/xj31a6/de/13577/exec.out 2> /data/asap2/users/1/xj31a6/de/13577/exec.err'" ## ---------------------------------------------------------------- ## Run 13578 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 $PROJECT_DIR/de/13578/" ## Running Differential expression [13578] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:16 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13578] [Differential expression #16 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:16 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13578 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13578 wilcox-seurat /layers/norm_2_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/xj31a6/de/13578/exec.out 2> /data/asap2/users/1/xj31a6/de/13578/exec.err'" ## ---------------------------------------------------------------- ## Run 13579 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 $PROJECT_DIR/de/13579/" ## Running Differential expression [13579] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:17 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13579] [Differential expression #17 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:17 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13579 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13579 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_17_wilcox-seurat null /col_attrs/_clust_1_seurat 17 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13579/exec.out 2> /data/asap2/users/1/xj31a6/de/13579/exec.err'" ## ---------------------------------------------------------------- ## Run 13580 Differential expression (Differential expression #18 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 $PROJECT_DIR/de/13580/" ## Running Differential expression [13580] [Differential expression #18 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:18 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13580] [Differential expression #18 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:18 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13580 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13580 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_18_wilcox-seurat null /col_attrs/_clust_1_seurat 18 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13580/exec.out 2> /data/asap2/users/1/xj31a6/de/13580/exec.err'" ## ---------------------------------------------------------------- ## Run 13581 Differential expression (Differential expression #19 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 $PROJECT_DIR/de/13581/" ## Running Differential expression [13581] [Differential expression #19 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:19 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13581] [Differential expression #19 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:19 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13581 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13581 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_19_wilcox-seurat null /col_attrs/_clust_1_seurat 19 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13581/exec.out 2> /data/asap2/users/1/xj31a6/de/13581/exec.err'" ## ---------------------------------------------------------------- ## Run 13582 Differential expression (Differential expression #20 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 $PROJECT_DIR/de/13582/" ## Running Differential expression [13582] [Differential expression #20 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:20 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13582] [Differential expression #20 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:20 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13582 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13582 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_20_wilcox-seurat null /col_attrs/_clust_1_seurat 20 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13582/exec.out 2> /data/asap2/users/1/xj31a6/de/13582/exec.err'" ## ---------------------------------------------------------------- ## Run 13583 Differential expression (Differential expression #21 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 $PROJECT_DIR/de/13583/" ## Running Differential expression [13583] [Differential expression #21 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:21 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13583] [Differential expression #21 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:21 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13583 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13583 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_21_wilcox-seurat null /col_attrs/_clust_1_seurat 21 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13583/exec.out 2> /data/asap2/users/1/xj31a6/de/13583/exec.err'" ## ---------------------------------------------------------------- ## Run 13584 Differential expression (Differential expression #22 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 $PROJECT_DIR/de/13584/" ## Running Differential expression [13584] [Differential expression #22 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:22 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13584] [Differential expression #22 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:22 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13584 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13584 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_22_wilcox-seurat null /col_attrs/_clust_1_seurat 22 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13584/exec.out 2> /data/asap2/users/1/xj31a6/de/13584/exec.err'" ## ---------------------------------------------------------------- ## Run 13585 Differential expression (Differential expression #23 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 $PROJECT_DIR/de/13585/" ## Running Differential expression [13585] [Differential expression #23 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:23 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13585] [Differential expression #23 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:23 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13585 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13585 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_23_wilcox-seurat null /col_attrs/_clust_1_seurat 23 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13585/exec.out 2> /data/asap2/users/1/xj31a6/de/13585/exec.err'" ## ---------------------------------------------------------------- ## Run 13586 Differential expression (Differential expression #24 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 $PROJECT_DIR/de/13586/" ## Running Differential expression [13586] [Differential expression #24 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:24 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13586] [Differential expression #24 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:24 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13586 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13586 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_24_wilcox-seurat null /col_attrs/_clust_1_seurat 24 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13586/exec.out 2> /data/asap2/users/1/xj31a6/de/13586/exec.err'" ## ---------------------------------------------------------------- ## Run 13587 Differential expression (Differential expression #25 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 $PROJECT_DIR/de/13587/" ## Running Differential expression [13587] [Differential expression #25 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:25 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13587] [Differential expression #25 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:25 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13587 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13587 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_25_wilcox-seurat null /col_attrs/_clust_1_seurat 25 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13587/exec.out 2> /data/asap2/users/1/xj31a6/de/13587/exec.err'" ## ---------------------------------------------------------------- ## Run 13588 Differential expression (Differential expression #26 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 $PROJECT_DIR/de/13588/" ## Running Differential expression [13588] [Differential expression #26 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:26 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13588] [Differential expression #26 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:26 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13588 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13588 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_26_wilcox-seurat null /col_attrs/_clust_1_seurat 26 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13588/exec.out 2> /data/asap2/users/1/xj31a6/de/13588/exec.err'" ## ---------------------------------------------------------------- ## Run 13589 Differential expression (Differential expression #27 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 $PROJECT_DIR/de/13589/" ## Running Differential expression [13589] [Differential expression #27 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:27 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13589] [Differential expression #27 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:27 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13589 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13589 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_27_wilcox-seurat null /col_attrs/_clust_1_seurat 27 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13589/exec.out 2> /data/asap2/users/1/xj31a6/de/13589/exec.err'" ## ---------------------------------------------------------------- ## Run 13590 Differential expression (Differential expression #28 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 $PROJECT_DIR/de/13590/" ## Running Differential expression [13590] [Differential expression #28 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:28 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13590] [Differential expression #28 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:28 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13590 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13590 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_28_wilcox-seurat null /col_attrs/_clust_1_seurat 28 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13590/exec.out 2> /data/asap2/users/1/xj31a6/de/13590/exec.err'" ## ---------------------------------------------------------------- ## Run 13591 Differential expression (Differential expression #29 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 $PROJECT_DIR/de/13591/" ## Running Differential expression [13591] [Differential expression #29 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:29 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13591] [Differential expression #29 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:29 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13591 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13591 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_29_wilcox-seurat null /col_attrs/_clust_1_seurat 29 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13591/exec.out 2> /data/asap2/users/1/xj31a6/de/13591/exec.err'" ## ---------------------------------------------------------------- ## Run 13592 Differential expression (Differential expression #30 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 $PROJECT_DIR/de/13592/" ## Running Differential expression [13592] [Differential expression #30 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:30 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13592] [Differential expression #30 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:30 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13592 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13592 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_30_wilcox-seurat null /col_attrs/_clust_1_seurat 30 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13592/exec.out 2> /data/asap2/users/1/xj31a6/de/13592/exec.err'" ## ---------------------------------------------------------------- ## Run 13593 Differential expression (Differential expression #31 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 $PROJECT_DIR/de/13593/" ## Running Differential expression [13593] [Differential expression #31 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:31 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13593] [Differential expression #31 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:31 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13593 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13593 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_31_wilcox-seurat null /col_attrs/_clust_1_seurat 31 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13593/exec.out 2> /data/asap2/users/1/xj31a6/de/13593/exec.err'" ## ---------------------------------------------------------------- ## Run 13594 Differential expression (Differential expression #32 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 $PROJECT_DIR/de/13594/" ## Running Differential expression [13594] [Differential expression #32 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:32 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13594] [Differential expression #32 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:32 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13594 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13594 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_32_wilcox-seurat null /col_attrs/_clust_1_seurat 32 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13594/exec.out 2> /data/asap2/users/1/xj31a6/de/13594/exec.err'" ## ---------------------------------------------------------------- ## Run 13595 Differential expression (Differential expression #33 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 $PROJECT_DIR/de/13595/" ## Running Differential expression [13595] [Differential expression #33 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:33 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13595] [Differential expression #33 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:33 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13595 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13595 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_33_wilcox-seurat null /col_attrs/_clust_1_seurat 33 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13595/exec.out 2> /data/asap2/users/1/xj31a6/de/13595/exec.err'" ## ---------------------------------------------------------------- ## Run 13596 Differential expression (Differential expression #34 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 $PROJECT_DIR/de/13596/" ## Running Differential expression [13596] [Differential expression #34 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:34 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13596] [Differential expression #34 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:34 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13596 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13596 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_34_wilcox-seurat null /col_attrs/_clust_1_seurat 34 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13596/exec.out 2> /data/asap2/users/1/xj31a6/de/13596/exec.err'" ## ---------------------------------------------------------------- ## Run 13597 Differential expression (Differential expression #35 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 $PROJECT_DIR/de/13597/" ## Running Differential expression [13597] [Differential expression #35 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:35 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:) echo '-> Running Differential expression [13597] [Differential expression #35 wilcox-seurat] (input_matrix:normalization #2 groups:clustering #1 group_ref:35 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:1.3 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_13597 --net=host -e HOST_USER_ID=$(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/xj31a6/gene_filtering/11121/output.loom /data/asap2/users/1/xj31a6/de/13597 wilcox-seurat /layers/norm_2_asap_seurat /row_attrs/_de_35_wilcox-seurat null /col_attrs/_clust_1_seurat 35 null false 0.1 null 1.3 null 1> /data/asap2/users/1/xj31a6/de/13597/exec.out 2> /data/asap2/users/1/xj31a6/de/13597/exec.err'"