## This script contains all commands executed in the PROJECT 2d1rq4 and can be run again using the ASAP_run docker (https://hub.docker.com/layers/fabdavid/asap_run) echo '*******************Reproducing analysis of PROJECT 2d1rq4 / ASAP93**********************' 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/2d1rq4 ## Pull Docker images (must run before any docker run in this script) docker pull fabdavid/asap_run:v5 ## Host LOOM staging directory (inside Docker volume) docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $LOOM_DIR; chmod 777 $LOOM_DIR" echo 'This project is PUBLIC => Nothing to do' ## Local PostgreSQL: create ASAP data database and load dump if missing if ! psql -lqt | cut -d \| -f 1 | grep -qw asap_data_v6; then echo 'Create database asap_data_v6'; echo '$PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v6'; $PSQL_DIR/createdb -p $ASAP_DATA_DB_PORT asap_data_v6; echo 'wget -qO - https://asap.epfl.ch/dumps/asap_data_v6.sql.gz | gunzip | grep -v \'AS integer\' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v6'; wget -qO - https://asap.epfl.ch/dumps/asap_data_v6.sql.gz | gunzip | grep -v 'AS integer' | $PSQL_DIR/psql -p $ASAP_DATA_DB_PORT asap_data_v6; fi ## Project directory on the shared volume docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR" ## Step output directories (one folder per pipeline step that has runs) docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/normalization/ && mkdir -p $PROJECT_DIR/scaling/ && mkdir -p $PROJECT_DIR/import_metadata/ && mkdir -p $PROJECT_DIR/cell_filtering/ && mkdir -p $PROJECT_DIR/parsing/ && mkdir -p $PROJECT_DIR/dim_reduction/ && mkdir -p $PROJECT_DIR/gene_filtering/ && mkdir -p $PROJECT_DIR/removing_covariates/ && mkdir -p $PROJECT_DIR/de/ && mkdir -p $PROJECT_DIR/clustering/ && mkdir -p $PROJECT_DIR/ge/ && mkdir -p $PROJECT_DIR/marker_enrich/ && mkdir -p $PROJECT_DIR/markers/" ## Parsed LOOM file (public: wget; private: place file then symlink as below) echo 'Loading parsed Loom file...' docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "wget -qO $PROJECT_DIR/parsing/output.loom 'https://asap.epfl.ch/projects/2d1rq4/get_file?filename=parsing/output.loom'" ## Re-execute each recorded run (parsing step is skipped; LOOM is already in place) ## ---------------------------------------------------------------- ## Run 376146 Import metadata (Import metadata #1 add_meta) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/import_metadata/376146/" ## Running Import metadata [376146] [Import metadata #1 add_meta] () echo '-> Running Import metadata [376146] [Import metadata #1 add_meta] ()' ## Command sh -c 'rake parse_metadata[145930] ' ## ---------------------------------------------------------------- ## Run 376147 Cell filtering (Cell filtering #2 qc_plots) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/cell_filtering/376147/" ## writing file $PROJECT_DIR/cell_filtering/376147/discarded_cols.json echo '-> writing file $PROJECT_DIR/cell_filtering/376147/discarded_cols.json' docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "echo '{"discarded_cols":["67","74","75","76","150","151","170","171","214","261","263","321","361","362","470","473","496","503","506","537","540","689","692","734","737","759","762","775","778","884","961","964","1009","1012","1044","1055","1058","1068","1071","1074","1077","1102","1265","1268","1401","1404","1497","1517","1520","1533","1536","1551","1554","1560","1563","1679","1682","1698","1701","1746","1749","1755","1915","1969","2068","2071","2144","2147","2187","2190","2215","2218","2308","2311","2325","2328","2362","2368","2372","2379","2399","2403","2409","2427","2430","2432","2435","2622","2631","2637","2640","2646","2733","2739","2752","2758","2866","2872","2910","3015","3023","3030","3089","3096","3142","3149","3163","3186","3194","3260","3283","3292","3342","3352","3362","3389","3399","3412","3444","3638","3646","3650","3658","3687","3699","3714","3726","3910","3922","3967","3970","3979","3988","4000","4039","4083","4251","4271","4284","4360","4386","4400","4453","4651","4728","4744","4754","4755","4772","4784","4786","4790","4801","4803","4949","4953","4957","4974","4990","5007","5011","5028","5060","5077","5092","5109","5119","5136","5152","5158","5169","5175","5232","5247","5249","5264","5313","5350","5365","5368","5426","5508","5527","5578","5597","5720","5727","5746","5750","5753","5767","5844","5927","5929","5932","5947","5952","5977","5997","6028","6051","6059","6063","6079","6083","6107","6127","6176","6196","6389","6409","6531","6548","6551","6568","6574","6594","6717","6737","6757","6767","6778","6820","6841","6946","6960","6981","7190","7211","7244","7245","7266","7291","7302","7308","7324","7330","7445","7536","7542","7581","7603","7817","7839","7847","7869","7973","7995","8003","8017","8038","8245","8563","8573","8598","8641","8654","8678","8947","8958","8974","8976","9002","9019","9030"]}' > $PROJECT_DIR/cell_filtering/376147/discarded_cols.json" ## writing file $PROJECT_DIR/cell_filtering/376147/manually_discarded_cols.json echo '-> writing file $PROJECT_DIR/cell_filtering/376147/manually_discarded_cols.json' docker run --net=host --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "echo '{"manually_discarded_cols":[67,74,75,76,150,151,170,171,214,261,263,321,361,362,470,473,496,503,506,537,540,689,692,734,737,759,762,775,778,884,961,964,1009,1012,1044,1055,1058,1068,1071,1074,1077,1102,1265,1268,1401,1404,1497,1517,1520,1533,1536,1551,1554,1560,1563,1679,1682,1698,1701,1746,1749,1755,1915,1969,2068,2071,2144,2147,2187,2190,2215,2218,2308,2311,2325,2328,2362,2368,2372,2379,2399,2403,2409,2427,2430,2432,2435,2622,2631,2637,2640,2646,2733,2739,2752,2758,2866,2872,2910,3015,3023,3030,3089,3096,3142,3149,3163,3186,3194,3260,3283,3292,3342,3352,3362,3389,3399,3412,3444,3638,3646,3650,3658,3687,3699,3714,3726,3910,3922,3967,3970,3979,3988,4000,4039,4083,4251,4271,4284,4360,4386,4400,4453,4651,4728,4744,4754,4755,4772,4784,4786,4790,4801,4803,4949,4953,4957,4974,4990,5007,5011,5028,5060,5077,5092,5109,5119,5136,5152,5158,5169,5175,5232,5247,5249,5264,5313,5350,5365,5368,5426,5508,5527,5578,5597,5720,5727,5746,5750,5753,5767,5844,5927,5929,5932,5947,5952,5977,5997,6028,6051,6059,6063,6079,6083,6107,6127,6176,6196,6389,6409,6531,6548,6551,6568,6574,6594,6717,6737,6757,6767,6778,6820,6841,6946,6960,6981,7190,7211,7244,7245,7266,7291,7302,7308,7324,7330,7445,7536,7542,7581,7603,7817,7839,7847,7869,7973,7995,8003,8017,8038,8245,8563,8573,8598,8641,8654,8678,8947,8958,8974,8976,9002,9019,9030]}' > $PROJECT_DIR/cell_filtering/376147/manually_discarded_cols.json" ## Running Cell filtering [376147] [Cell filtering #2 qc_plots] (manual_selection:/col_attrs/Cells to keep: kept=1 depth:1000 detected_genes:1000 protein_coding_content:80 mito_content:20 ribo_content:40 nber_manually_discarded_cols:265 input_matrix:parsing) echo '-> Running Cell filtering [376147] [Cell filtering #2 qc_plots] (manual_selection:/col_attrs/Cells to keep: kept=1 depth:1000 detected_genes:1000 protein_coding_content:80 mito_content:20 ribo_content:40 nber_manually_discarded_cols:265 input_matrix:parsing)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376147 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterCols -loom /data/asap2/users/776/2d1rq4/parsing/output.loom -o /data/asap2/users/776/2d1rq4/cell_filtering/145933 -col_indexes_file /data/asap2/users/776/2d1rq4/cell_filtering/376147/discarded_cols.json 1> /data/asap2/users/776/z43acg/cell_filtering/145933/exec.out 2> /data/asap2/users/776/z43acg/cell_filtering/145933/exec.err'" ## ---------------------------------------------------------------- ## Run 376148 Gene filtering (Gene filtering #1 cpm) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/gene_filtering/376148/" ## Running Gene filtering [376148] [Gene filtering #1 cpm] (input_matrix:cell_filtering #2 min_cpm_per_cell:1 nber_detected_cells:4) echo '-> Running Gene filtering [376148] [Gene filtering #1 cpm] (input_matrix:cell_filtering #2 min_cpm_per_cell:1 nber_detected_cells:4)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376148 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FilterRows -loom /data/asap2/users/776/2d1rq4/cell_filtering/376147/output.loom -o /data/asap2/users/776/2d1rq4/gene_filtering/145934 -m cpm 1 4 1> /data/asap2/users/776/z43acg/gene_filtering/145934/exec.out 2> /data/asap2/users/776/z43acg/gene_filtering/145934/exec.err'" ## ---------------------------------------------------------------- ## Run 376149 Normalization (Normalization #1 asap_seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/normalization/376149/" ## Running Normalization [376149] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000) echo '-> Running Normalization [376149] [Normalization #1 asap_seurat] (input_matrix:gene_filtering #1 scale_factor:10000)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376149 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Normalization -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -o /data/asap2/users/776/2d1rq4/normalization/376149/output.json -oAnnot /layers/norm_1_asap_seurat -scaleFactor 10000 1> /data/asap2/users/776/z43acg/normalization/145935/exec.out 2> /data/asap2/users/776/z43acg/normalization/145935/exec.err'" ## ---------------------------------------------------------------- ## Run 376150 Import metadata (Import metadata #2 add_meta) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/import_metadata/376150/" ## Running Import metadata [376150] [Import metadata #2 add_meta] () echo '-> Running Import metadata [376150] [Import metadata #2 add_meta] ()' ## Command sh -c 'rake parse_metadata[145936] ' ## ---------------------------------------------------------------- ## Run 376151 Removing covariates (Removing covariates #1 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/removing_covariates/376151/" ## Running Removing covariates [376151] [Removing covariates #1 limma] (input_matrix:normalization #1 covariates:import_metadata #2) echo '-> Running Removing covariates [376151] [Removing covariates #1 limma] (input_matrix:normalization #1 covariates:import_metadata #2)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376151 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla batch.asap.2.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/removing_covariates/145937 limma /layers/norm_1_asap_seurat /layers/rmcov_1_limma /col_attrs/Batch 1> /data/asap2/users/776/z43acg/removing_covariates/145937/exec.out 2> /data/asap2/users/776/z43acg/removing_covariates/145937/exec.err'" ## ---------------------------------------------------------------- ## Run 376152 Scaling (Scaling #1 asap_seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/scaling/376152/" ## Running Scaling [376152] [Scaling #1 asap_seurat] (input_matrix:normalization #1 do_scale:true do_center:true scale_max:10) echo '-> Running Scaling [376152] [Scaling #1 asap_seurat] (input_matrix:normalization #1 do_scale:true do_center:true scale_max:10)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376152 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Scaling -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -o /data/asap2/users/776/2d1rq4/scaling/376152/output.json -iAnnot /layers/norm_1_asap_seurat -oAnnot /layers/scaling_1_asap_seurat -scale true -center true -scaleMax 10 1> /data/asap2/users/776/z43acg/scaling/145938/exec.out 2> /data/asap2/users/776/z43acg/scaling/145938/exec.err'" ## ---------------------------------------------------------------- ## Run 376153 Scaling (Scaling #2 asap_seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/scaling/376153/" ## Running Scaling [376153] [Scaling #2 asap_seurat] (input_matrix:removing_covariates #1 do_scale:true do_center:true scale_max:10) echo '-> Running Scaling [376153] [Scaling #2 asap_seurat] (input_matrix:removing_covariates #1 do_scale:true do_center:true scale_max:10)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376153 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Scaling -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -o /data/asap2/users/776/2d1rq4/scaling/376153/output.json -iAnnot /layers/rmcov_1_limma -oAnnot /layers/scaling_2_asap_seurat -scale true -center true -scaleMax 10 1> /data/asap2/users/776/z43acg/scaling/145939/exec.out 2> /data/asap2/users/776/z43acg/scaling/145939/exec.err'" ## ---------------------------------------------------------------- ## Run 376154 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:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/376154/" ## Running Dimension reduction [376154] [Dimension reduction #3 umap] (input_matrix:scaling #2 nber_dims:2 min_dist:0.01 n_neighbors:10 metric:correlation) echo '-> Running Dimension reduction [376154] [Dimension reduction #3 umap] (input_matrix:scaling #2 nber_dims:2 min_dist:0.01 n_neighbors:10 metric:correlation)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376154 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/dim_reduction/145947 umap /layers/scaling_2_asap_seurat /col_attrs/_dr_3_umap_2D 2 0.01 10 correlation 1> /data/asap2/users/776/z43acg/dim_reduction/145947/exec.out 2> /data/asap2/users/776/z43acg/dim_reduction/145947/exec.err'" ## ---------------------------------------------------------------- ## Run 376155 Dimension reduction (Dimension reduction #4 umap) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/dim_reduction/376155/" ## Running Dimension reduction [376155] [Dimension reduction #4 umap] (input_matrix:scaling #2 nber_dims:3 min_dist:0.01 n_neighbors:10 metric:correlation) echo '-> Running Dimension reduction [376155] [Dimension reduction #4 umap] (input_matrix:scaling #2 nber_dims:3 min_dist:0.01 n_neighbors:10 metric:correlation)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376155 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla dimension_reduction.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/dim_reduction/145948 umap /layers/scaling_2_asap_seurat /col_attrs/_dr_4_umap_3D 3 0.01 10 correlation 1> /data/asap2/users/776/z43acg/dim_reduction/145948/exec.out 2> /data/asap2/users/776/z43acg/dim_reduction/145948/exec.err'" ## ---------------------------------------------------------------- ## Run 376156 Clustering (Clustering #1 seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/clustering/376156/" ## Running Clustering [376156] [Clustering #1 seurat] (input_matrix:dim_reduction #3 k:20 resolution:0.4 algorithm:louvain graph_type:snn) echo '-> Running Clustering [376156] [Clustering #1 seurat] (input_matrix:dim_reduction #3 k:20 resolution:0.4 algorithm:louvain graph_type:snn)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376156 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla clustering.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/clustering/145949 seurat /col_attrs/_dr_3_umap_2D /col_attrs/_clust_1_seurat 20 0.4 louvain snn 1> /data/asap2/users/776/z43acg/clustering/145949/exec.out 2> /data/asap2/users/776/z43acg/clustering/145949/exec.err'" ## ---------------------------------------------------------------- ## Run 376157 Import metadata (Import metadata #3 add_meta) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/import_metadata/376157/" ## Running Import metadata [376157] [Import metadata #3 add_meta] () echo '-> Running Import metadata [376157] [Import metadata #3 add_meta] ()' ## Command sh -c 'rake parse_metadata[146122] ' ## ---------------------------------------------------------------- ## Run 376158 Differential expression (Differential expression #1 wilcox_seurat) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376158/" ## Running Differential expression [376158] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376158] [Differential expression #1 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:1 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376158 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146123 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 0 null 16 1> /data/asap2/users/776/z43acg/de/146123/exec.out 2> /data/asap2/users/776/z43acg/de/146123/exec.err'" ## ---------------------------------------------------------------- ## Run 376159 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:v5 -c "mkdir -p $PROJECT_DIR/de/376159/" ## Running Differential expression [376159] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:10 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376159] [Differential expression #2 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:10 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376159 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146124 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_2_wilcox_seurat null /col_attrs/_clust_1_seurat 10 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146124/exec.out 2> /data/asap2/users/776/z43acg/de/146124/exec.err'" ## ---------------------------------------------------------------- ## Run 376160 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:v5 -c "mkdir -p $PROJECT_DIR/de/376160/" ## Running Differential expression [376160] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:11 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376160] [Differential expression #3 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:11 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376160 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146125 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_3_wilcox_seurat null /col_attrs/_clust_1_seurat 11 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146125/exec.out 2> /data/asap2/users/776/z43acg/de/146125/exec.err'" ## ---------------------------------------------------------------- ## Run 376161 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:v5 -c "mkdir -p $PROJECT_DIR/de/376161/" ## Running Differential expression [376161] [Differential expression #4 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376161] [Differential expression #4 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:12 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376161 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146126 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_4_wilcox_seurat null /col_attrs/_clust_1_seurat 12 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146126/exec.out 2> /data/asap2/users/776/z43acg/de/146126/exec.err'" ## ---------------------------------------------------------------- ## Run 376162 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:v5 -c "mkdir -p $PROJECT_DIR/de/376162/" ## Running Differential expression [376162] [Differential expression #5 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:13 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376162] [Differential expression #5 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:13 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376162 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146127 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_5_wilcox_seurat null /col_attrs/_clust_1_seurat 13 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146127/exec.out 2> /data/asap2/users/776/z43acg/de/146127/exec.err'" ## ---------------------------------------------------------------- ## Run 376163 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:v5 -c "mkdir -p $PROJECT_DIR/de/376163/" ## Running Differential expression [376163] [Differential expression #6 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376163] [Differential expression #6 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:14 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376163 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146128 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_6_wilcox_seurat null /col_attrs/_clust_1_seurat 14 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146128/exec.out 2> /data/asap2/users/776/z43acg/de/146128/exec.err'" ## ---------------------------------------------------------------- ## Run 376164 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:v5 -c "mkdir -p $PROJECT_DIR/de/376164/" ## Running Differential expression [376164] [Differential expression #7 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376164] [Differential expression #7 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:15 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376164 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146129 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_7_wilcox_seurat null /col_attrs/_clust_1_seurat 15 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146129/exec.out 2> /data/asap2/users/776/z43acg/de/146129/exec.err'" ## ---------------------------------------------------------------- ## Run 376165 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:v5 -c "mkdir -p $PROJECT_DIR/de/376165/" ## Running Differential expression [376165] [Differential expression #8 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:16 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376165] [Differential expression #8 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:16 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376165 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146130 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_8_wilcox_seurat null /col_attrs/_clust_1_seurat 16 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146130/exec.out 2> /data/asap2/users/776/z43acg/de/146130/exec.err'" ## ---------------------------------------------------------------- ## Run 376166 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:v5 -c "mkdir -p $PROJECT_DIR/de/376166/" ## Running Differential expression [376166] [Differential expression #9 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:17 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376166] [Differential expression #9 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:17 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376166 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146131 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_9_wilcox_seurat null /col_attrs/_clust_1_seurat 17 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146131/exec.out 2> /data/asap2/users/776/z43acg/de/146131/exec.err'" ## ---------------------------------------------------------------- ## Run 376167 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:v5 -c "mkdir -p $PROJECT_DIR/de/376167/" ## Running Differential expression [376167] [Differential expression #10 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:18 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376167] [Differential expression #10 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:18 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376167 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146132 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_10_wilcox_seurat null /col_attrs/_clust_1_seurat 18 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146132/exec.out 2> /data/asap2/users/776/z43acg/de/146132/exec.err'" ## ---------------------------------------------------------------- ## Run 376168 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:v5 -c "mkdir -p $PROJECT_DIR/de/376168/" ## Running Differential expression [376168] [Differential expression #11 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:2 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376168] [Differential expression #11 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:2 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376168 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146133 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_11_wilcox_seurat null /col_attrs/_clust_1_seurat 2 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146133/exec.out 2> /data/asap2/users/776/z43acg/de/146133/exec.err'" ## ---------------------------------------------------------------- ## Run 376169 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:v5 -c "mkdir -p $PROJECT_DIR/de/376169/" ## Running Differential expression [376169] [Differential expression #12 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:3 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376169] [Differential expression #12 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:3 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376169 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146134 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_12_wilcox_seurat null /col_attrs/_clust_1_seurat 3 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146134/exec.out 2> /data/asap2/users/776/z43acg/de/146134/exec.err'" ## ---------------------------------------------------------------- ## Run 376170 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:v5 -c "mkdir -p $PROJECT_DIR/de/376170/" ## Running Differential expression [376170] [Differential expression #13 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:4 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376170] [Differential expression #13 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:4 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376170 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146135 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_13_wilcox_seurat null /col_attrs/_clust_1_seurat 4 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146135/exec.out 2> /data/asap2/users/776/z43acg/de/146135/exec.err'" ## ---------------------------------------------------------------- ## Run 376171 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:v5 -c "mkdir -p $PROJECT_DIR/de/376171/" ## Running Differential expression [376171] [Differential expression #14 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:5 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376171] [Differential expression #14 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:5 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376171 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146136 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_14_wilcox_seurat null /col_attrs/_clust_1_seurat 5 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146136/exec.out 2> /data/asap2/users/776/z43acg/de/146136/exec.err'" ## ---------------------------------------------------------------- ## Run 376172 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:v5 -c "mkdir -p $PROJECT_DIR/de/376172/" ## Running Differential expression [376172] [Differential expression #15 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376172] [Differential expression #15 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:6 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376172 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146137 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_15_wilcox_seurat null /col_attrs/_clust_1_seurat 6 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146137/exec.out 2> /data/asap2/users/776/z43acg/de/146137/exec.err'" ## ---------------------------------------------------------------- ## Run 376173 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:v5 -c "mkdir -p $PROJECT_DIR/de/376173/" ## Running Differential expression [376173] [Differential expression #16 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:7 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376173] [Differential expression #16 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:7 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376173 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146138 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_16_wilcox_seurat null /col_attrs/_clust_1_seurat 7 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146138/exec.out 2> /data/asap2/users/776/z43acg/de/146138/exec.err'" ## ---------------------------------------------------------------- ## Run 376174 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:v5 -c "mkdir -p $PROJECT_DIR/de/376174/" ## Running Differential expression [376174] [Differential expression #17 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:8 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376174] [Differential expression #17 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:8 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376174 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146139 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_17_wilcox_seurat null /col_attrs/_clust_1_seurat 8 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146139/exec.out 2> /data/asap2/users/776/z43acg/de/146139/exec.err'" ## ---------------------------------------------------------------- ## Run 376175 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:v5 -c "mkdir -p $PROJECT_DIR/de/376175/" ## Running Differential expression [376175] [Differential expression #18 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376175] [Differential expression #18 wilcox_seurat] (input_matrix:normalization #1 groups:clustering #1 group_ref:9 group_comp: min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376175 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146140 wilcox_seurat /layers/norm_1_asap_seurat /row_attrs/_de_18_wilcox_seurat null /col_attrs/_clust_1_seurat 9 null false 0.1 null 0 null 16 1> /data/asap2/users/776/z43acg/de/146140/exec.out 2> /data/asap2/users/776/z43acg/de/146140/exec.err'" ## ---------------------------------------------------------------- ## Run 376176 Differential expression (Differential expression #19 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376176/" ## Running Differential expression [376176] [Differential expression #19 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:Alpha SorCS2 group_comp:Alpha WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376176] [Differential expression #19 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:Alpha SorCS2 group_comp:Alpha WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376176 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146141 limma /layers/norm_1_asap_seurat /row_attrs/_de_19_limma /col_attrs/Batch /col_attrs/CellType_genotype \"Alpha SorCS2\" \"Alpha WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146141/exec.out 2> /data/asap2/users/776/z43acg/de/146141/exec.err'" ## ---------------------------------------------------------------- ## Run 376177 Differential expression (Differential expression #20 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376177/" ## Running Differential expression [376177] [Differential expression #20 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:Beta ? SorCS2 group_comp:Beta ? WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376177] [Differential expression #20 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:Beta ? SorCS2 group_comp:Beta ? WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376177 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146174 limma /layers/norm_1_asap_seurat /row_attrs/_de_20_limma /col_attrs/Batch /col_attrs/CellType_genotype \"Beta ? SorCS2\" \"Beta ? WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146174/exec.out 2> /data/asap2/users/776/z43acg/de/146174/exec.err'" ## ---------------------------------------------------------------- ## Run 376178 Differential expression (Differential expression #21 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376178/" ## Running Differential expression [376178] [Differential expression #21 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:Beta SorCS2 group_comp:Beta WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376178] [Differential expression #21 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:Beta SorCS2 group_comp:Beta WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376178 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146175 limma /layers/norm_1_asap_seurat /row_attrs/_de_21_limma /col_attrs/Batch /col_attrs/CellType_genotype \"Beta SorCS2\" \"Beta WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146175/exec.out 2> /data/asap2/users/776/z43acg/de/146175/exec.err'" ## ---------------------------------------------------------------- ## Run 376179 Differential expression (Differential expression #22 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376179/" ## Running Differential expression [376179] [Differential expression #22 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:Delta SorCS2 group_comp:Delta WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376179] [Differential expression #22 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:Delta SorCS2 group_comp:Delta WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376179 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146176 limma /layers/norm_1_asap_seurat /row_attrs/_de_22_limma /col_attrs/Batch /col_attrs/CellType_genotype \"Delta SorCS2\" \"Delta WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146176/exec.out 2> /data/asap2/users/776/z43acg/de/146176/exec.err'" ## ---------------------------------------------------------------- ## Run 376180 Differential expression (Differential expression #23 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376180/" ## Running Differential expression [376180] [Differential expression #23 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:PP SorCS2 group_comp:PP WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376180] [Differential expression #23 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:PP SorCS2 group_comp:PP WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376180 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146177 limma /layers/norm_1_asap_seurat /row_attrs/_de_23_limma /col_attrs/Batch /col_attrs/CellType_genotype \"PP SorCS2\" \"PP WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146177/exec.out 2> /data/asap2/users/776/z43acg/de/146177/exec.err'" ## ---------------------------------------------------------------- ## Run 376181 Differential expression (Differential expression #24 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376181/" ## Running Differential expression [376181] [Differential expression #24 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:1 SorCS2 group_comp:1 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376181] [Differential expression #24 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:1 SorCS2 group_comp:1 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376181 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146178 limma /layers/norm_1_asap_seurat /row_attrs/_de_24_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"1 SorCS2\" \"1 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146178/exec.out 2> /data/asap2/users/776/z43acg/de/146178/exec.err'" ## ---------------------------------------------------------------- ## Run 376182 Differential expression (Differential expression #25 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376182/" ## Running Differential expression [376182] [Differential expression #25 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:10 SorCS2 group_comp:10 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376182] [Differential expression #25 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:10 SorCS2 group_comp:10 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376182 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146179 limma /layers/norm_1_asap_seurat /row_attrs/_de_25_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"10 SorCS2\" \"10 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146179/exec.out 2> /data/asap2/users/776/z43acg/de/146179/exec.err'" ## ---------------------------------------------------------------- ## Run 376183 Differential expression (Differential expression #26 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376183/" ## Running Differential expression [376183] [Differential expression #26 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:11 SorCS2 group_comp:11 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376183] [Differential expression #26 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:11 SorCS2 group_comp:11 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376183 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146180 limma /layers/norm_1_asap_seurat /row_attrs/_de_26_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"11 SorCS2\" \"11 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146180/exec.out 2> /data/asap2/users/776/z43acg/de/146180/exec.err'" ## ---------------------------------------------------------------- ## Run 376184 Differential expression (Differential expression #27 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376184/" ## Running Differential expression [376184] [Differential expression #27 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:12 SorCS2 group_comp:12 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376184] [Differential expression #27 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:12 SorCS2 group_comp:12 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376184 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146181 limma /layers/norm_1_asap_seurat /row_attrs/_de_27_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"12 SorCS2\" \"12 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146181/exec.out 2> /data/asap2/users/776/z43acg/de/146181/exec.err'" ## ---------------------------------------------------------------- ## Run 376185 Differential expression (Differential expression #28 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376185/" ## Running Differential expression [376185] [Differential expression #28 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:13 SorCS2 group_comp:13 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376185] [Differential expression #28 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:13 SorCS2 group_comp:13 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376185 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146182 limma /layers/norm_1_asap_seurat /row_attrs/_de_28_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"13 SorCS2\" \"13 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146182/exec.out 2> /data/asap2/users/776/z43acg/de/146182/exec.err'" ## ---------------------------------------------------------------- ## Run 376186 Differential expression (Differential expression #29 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376186/" ## Running Differential expression [376186] [Differential expression #29 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:14 SorCS2 group_comp:14 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376186] [Differential expression #29 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:14 SorCS2 group_comp:14 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376186 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146183 limma /layers/norm_1_asap_seurat /row_attrs/_de_29_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"14 SorCS2\" \"14 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146183/exec.out 2> /data/asap2/users/776/z43acg/de/146183/exec.err'" ## ---------------------------------------------------------------- ## Run 376187 Differential expression (Differential expression #30 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376187/" ## Running Differential expression [376187] [Differential expression #30 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:15 SorCS2 group_comp:15 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376187] [Differential expression #30 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:15 SorCS2 group_comp:15 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376187 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146184 limma /layers/norm_1_asap_seurat /row_attrs/_de_30_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"15 SorCS2\" \"15 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146184/exec.out 2> /data/asap2/users/776/z43acg/de/146184/exec.err'" ## ---------------------------------------------------------------- ## Run 376188 Differential expression (Differential expression #31 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376188/" ## Running Differential expression [376188] [Differential expression #31 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:16 SorCS2 group_comp:16 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376188] [Differential expression #31 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:16 SorCS2 group_comp:16 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376188 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146185 limma /layers/norm_1_asap_seurat /row_attrs/_de_31_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"16 SorCS2\" \"16 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146185/exec.out 2> /data/asap2/users/776/z43acg/de/146185/exec.err'" ## ---------------------------------------------------------------- ## Run 376189 Differential expression (Differential expression #32 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376189/" ## Running Differential expression [376189] [Differential expression #32 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:17 SorCS2 group_comp:17 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376189] [Differential expression #32 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:17 SorCS2 group_comp:17 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376189 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146186 limma /layers/norm_1_asap_seurat /row_attrs/_de_32_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"17 SorCS2\" \"17 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146186/exec.out 2> /data/asap2/users/776/z43acg/de/146186/exec.err'" ## ---------------------------------------------------------------- ## Run 376190 Differential expression (Differential expression #33 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376190/" ## Running Differential expression [376190] [Differential expression #33 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:18 SorCS2 group_comp:18 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376190] [Differential expression #33 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:18 SorCS2 group_comp:18 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376190 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146187 limma /layers/norm_1_asap_seurat /row_attrs/_de_33_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"18 SorCS2\" \"18 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146187/exec.out 2> /data/asap2/users/776/z43acg/de/146187/exec.err'" ## ---------------------------------------------------------------- ## Run 376191 Differential expression (Differential expression #34 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376191/" ## Running Differential expression [376191] [Differential expression #34 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:2 SorCS2 group_comp:2 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376191] [Differential expression #34 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:2 SorCS2 group_comp:2 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376191 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146188 limma /layers/norm_1_asap_seurat /row_attrs/_de_34_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"2 SorCS2\" \"2 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146188/exec.out 2> /data/asap2/users/776/z43acg/de/146188/exec.err'" ## ---------------------------------------------------------------- ## Run 376192 Differential expression (Differential expression #35 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376192/" ## Running Differential expression [376192] [Differential expression #35 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:3 SorCS2 group_comp:3 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376192] [Differential expression #35 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:3 SorCS2 group_comp:3 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376192 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146189 limma /layers/norm_1_asap_seurat /row_attrs/_de_35_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"3 SorCS2\" \"3 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146189/exec.out 2> /data/asap2/users/776/z43acg/de/146189/exec.err'" ## ---------------------------------------------------------------- ## Run 376193 Differential expression (Differential expression #36 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376193/" ## Running Differential expression [376193] [Differential expression #36 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:4 SorCS2 group_comp:4 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376193] [Differential expression #36 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:4 SorCS2 group_comp:4 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376193 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146190 limma /layers/norm_1_asap_seurat /row_attrs/_de_36_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"4 SorCS2\" \"4 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146190/exec.out 2> /data/asap2/users/776/z43acg/de/146190/exec.err'" ## ---------------------------------------------------------------- ## Run 376194 Differential expression (Differential expression #37 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376194/" ## Running Differential expression [376194] [Differential expression #37 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:5 SorCS2 group_comp:5 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376194] [Differential expression #37 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:5 SorCS2 group_comp:5 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376194 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146191 limma /layers/norm_1_asap_seurat /row_attrs/_de_37_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"5 SorCS2\" \"5 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146191/exec.out 2> /data/asap2/users/776/z43acg/de/146191/exec.err'" ## ---------------------------------------------------------------- ## Run 376195 Differential expression (Differential expression #38 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376195/" ## Running Differential expression [376195] [Differential expression #38 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:6 SorCS2 group_comp:6 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376195] [Differential expression #38 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:6 SorCS2 group_comp:6 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376195 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146192 limma /layers/norm_1_asap_seurat /row_attrs/_de_38_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"6 SorCS2\" \"6 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146192/exec.out 2> /data/asap2/users/776/z43acg/de/146192/exec.err'" ## ---------------------------------------------------------------- ## Run 376196 Differential expression (Differential expression #39 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376196/" ## Running Differential expression [376196] [Differential expression #39 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:7 SorCS2 group_comp:7 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376196] [Differential expression #39 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:7 SorCS2 group_comp:7 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376196 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146193 limma /layers/norm_1_asap_seurat /row_attrs/_de_39_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"7 SorCS2\" \"7 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146193/exec.out 2> /data/asap2/users/776/z43acg/de/146193/exec.err'" ## ---------------------------------------------------------------- ## Run 376197 Differential expression (Differential expression #40 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376197/" ## Running Differential expression [376197] [Differential expression #40 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:8 SorCS2 group_comp:8 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376197] [Differential expression #40 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:8 SorCS2 group_comp:8 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376197 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146194 limma /layers/norm_1_asap_seurat /row_attrs/_de_40_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"8 SorCS2\" \"8 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146194/exec.out 2> /data/asap2/users/776/z43acg/de/146194/exec.err'" ## ---------------------------------------------------------------- ## Run 376198 Differential expression (Differential expression #41 limma) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/de/376198/" ## Running Differential expression [376198] [Differential expression #41 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:9 SorCS2 group_comp:9 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:) echo '-> Running Differential expression [376198] [Differential expression #41 limma] (input_matrix:normalization #1 covariates:import_metadata #2 groups:import_metadata #3 group_ref:9 SorCS2 group_comp:9 WT min_pct:0.1 min_diff_pct: fc_threshold:0 max_cells_per_ident:)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376198 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'Rscript --vanilla de.R /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom /data/asap2/users/776/2d1rq4/de/146195 limma /layers/norm_1_asap_seurat /row_attrs/_de_41_limma /col_attrs/Batch /col_attrs/Cluster_Genotype \"9 SorCS2\" \"9 WT\" false 0.1 null 0 null 1> /data/asap2/users/776/z43acg/de/146195/exec.out 2> /data/asap2/users/776/z43acg/de/146195/exec.err'" ## ---------------------------------------------------------------- ## Run 376199 Find markers (Find markers #1 asap_markers) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/376199/" ## Running Find markers [376199] [Find markers #1 asap_markers] () echo '-> Running Find markers [376199] [Find markers #1 asap_markers] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376199 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -o /data/asap2/users/776/2d1rq4/markers/265865 --iAnnot /col_attrs/_clust_1_seurat --id 2315367 --is_count_table 1> /data/asap2/users/776/xpeef9/markers/265865/exec.out 2> /data/asap2/users/776/xpeef9/markers/265865/exec.err'" ## ---------------------------------------------------------------- ## Run 376200 Marker enrichment (Marker enrichment #2 asap_marker_enrichment) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/376200/" ## Running Marker enrichment [376200] [Marker enrichment #2 asap_marker_enrichment] () echo '-> Running Marker enrichment [376200] [Marker enrichment #2 asap_marker_enrichment] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376200 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/776/2d1rq4/markers/265865 -o /data/asap2/users/776/2d1rq4/markers/265866 --genesets 58,60,59,2091,57,2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/xpeef9/markers/265866/exec.out 2> /data/asap2/users/776/xpeef9/markers/265866/exec.err'" ## ---------------------------------------------------------------- ## Run 376201 Find markers (Find markers #2 asap_markers) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/376201/" ## Running Find markers [376201] [Find markers #2 asap_markers] () echo '-> Running Find markers [376201] [Find markers #2 asap_markers] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376201 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -o /data/asap2/users/776/2d1rq4/markers/265912 --iAnnot /col_attrs/CellType_genotype --id 2315375 --is_count_table 1> /data/asap2/users/776/xpeef9/markers/265912/exec.out 2> /data/asap2/users/776/xpeef9/markers/265912/exec.err'" ## ---------------------------------------------------------------- ## Run 376202 Marker enrichment (Marker enrichment #3 asap_marker_enrichment) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/376202/" ## Running Marker enrichment [376202] [Marker enrichment #3 asap_marker_enrichment] () echo '-> Running Marker enrichment [376202] [Marker enrichment #3 asap_marker_enrichment] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376202 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/776/2d1rq4/markers/265912 -o /data/asap2/users/776/2d1rq4/markers/265913 --genesets 58,60,59,2091,57,2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/xpeef9/markers/265913/exec.out 2> /data/asap2/users/776/xpeef9/markers/265913/exec.err'" ## ---------------------------------------------------------------- ## Run 376203 Find markers (Find markers #3 asap_markers) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/376203/" ## Running Find markers [376203] [Find markers #3 asap_markers] () echo '-> Running Find markers [376203] [Find markers #3 asap_markers] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376203 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -o /data/asap2/users/776/2d1rq4/markers/265914 --iAnnot /col_attrs/Cluster_Genotype --id 2315374 --is_count_table 1> /data/asap2/users/776/xpeef9/markers/265914/exec.out 2> /data/asap2/users/776/xpeef9/markers/265914/exec.err'" ## ---------------------------------------------------------------- ## Run 376204 Marker enrichment (Marker enrichment #4 asap_marker_enrichment) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/376204/" ## Running Marker enrichment [376204] [Marker enrichment #4 asap_marker_enrichment] () echo '-> Running Marker enrichment [376204] [Marker enrichment #4 asap_marker_enrichment] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376204 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/776/2d1rq4/markers/265914 -o /data/asap2/users/776/2d1rq4/markers/265915 --genesets 58,60,59,2091,57,2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/xpeef9/markers/265915/exec.out 2> /data/asap2/users/776/xpeef9/markers/265915/exec.err'" ## ---------------------------------------------------------------- ## Run 376205 Gene Enrichment (Gene Enrichment #1 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/376205/" ## Running Gene Enrichment [376205] [Gene Enrichment #1 basic] (input_de:de #19 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [376205] [Gene Enrichment #1 basic] (input_de:de #19 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376205 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -m fet -f /data/asap2/users/776/2d1rq4/tmp/872_376176_1_0.05_filtered_ids.json -o /data/asap2/users/776/2d1rq4/ge/376205/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/2d1rq4/ge/376205/exec.out 2> /data/asap2/users/776/2d1rq4/ge/376205/exec.err'" ## ---------------------------------------------------------------- ## Run 376206 Gene Enrichment (Gene Enrichment #2 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/376206/" ## Running Gene Enrichment [376206] [Gene Enrichment #2 basic] (input_de:de #20 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [376206] [Gene Enrichment #2 basic] (input_de:de #20 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376206 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -m fet -f /data/asap2/users/776/2d1rq4/tmp/872_376177_1_0.05_filtered_ids.json -o /data/asap2/users/776/2d1rq4/ge/376206/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/2d1rq4/ge/376206/exec.out 2> /data/asap2/users/776/2d1rq4/ge/376206/exec.err'" ## ---------------------------------------------------------------- ## Run 376207 Gene Enrichment (Gene Enrichment #3 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/376207/" ## Running Gene Enrichment [376207] [Gene Enrichment #3 basic] (input_de:de #21 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [376207] [Gene Enrichment #3 basic] (input_de:de #21 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376207 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -m fet -f /data/asap2/users/776/2d1rq4/tmp/872_376178_1_0.05_filtered_ids.json -o /data/asap2/users/776/2d1rq4/ge/376207/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/2d1rq4/ge/376207/exec.out 2> /data/asap2/users/776/2d1rq4/ge/376207/exec.err'" ## ---------------------------------------------------------------- ## Run 376208 Gene Enrichment (Gene Enrichment #4 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/376208/" ## Running Gene Enrichment [376208] [Gene Enrichment #4 basic] (input_de:de #22 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [376208] [Gene Enrichment #4 basic] (input_de:de #22 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376208 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -m fet -f /data/asap2/users/776/2d1rq4/tmp/872_376179_1_0.05_filtered_ids.json -o /data/asap2/users/776/2d1rq4/ge/376208/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/2d1rq4/ge/376208/exec.out 2> /data/asap2/users/776/2d1rq4/ge/376208/exec.err'" ## ---------------------------------------------------------------- ## Run 376209 Gene Enrichment (Gene Enrichment #5 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/376209/" ## Running Gene Enrichment [376209] [Gene Enrichment #5 basic] (input_de:de #23 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [376209] [Gene Enrichment #5 basic] (input_de:de #23 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376209 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -m fet -f /data/asap2/users/776/2d1rq4/tmp/872_376180_1_0.05_filtered_ids.json -o /data/asap2/users/776/2d1rq4/ge/376209/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/2d1rq4/ge/376209/exec.out 2> /data/asap2/users/776/2d1rq4/ge/376209/exec.err'" ## ---------------------------------------------------------------- ## Run 376210 Gene Enrichment (Gene Enrichment #6 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/376210/" ## Running Gene Enrichment [376210] [Gene Enrichment #6 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [376210] [Gene Enrichment #6 basic] (input_de:de #12 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376210 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -m fet -f /data/asap2/users/776/2d1rq4/tmp/872_376169_1_0.05_filtered_ids.json -o /data/asap2/users/776/2d1rq4/ge/376210/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/2d1rq4/ge/376210/exec.out 2> /data/asap2/users/776/2d1rq4/ge/376210/exec.err'" ## ---------------------------------------------------------------- ## Run 376211 Gene Enrichment (Gene Enrichment #7 basic) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/ge/376211/" ## Running Gene Enrichment [376211] [Gene Enrichment #7 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500) echo '-> Running Gene Enrichment [376211] [Gene Enrichment #7 basic] (input_de:de #13 fdr_cutoff:0.05 fc_cutoff:1 adj_method:fdr min:15 max:500)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376211 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T Enrichment -loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -m fet -f /data/asap2/users/776/2d1rq4/tmp/872_376170_1_0.05_filtered_ids.json -o /data/asap2/users/776/2d1rq4/ge/376211/output.json -max 500 -min 15 -adj fdr -geneset 58 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/2d1rq4/ge/376211/exec.out 2> /data/asap2/users/776/2d1rq4/ge/376211/exec.err'" ## ---------------------------------------------------------------- ## Run 376212 Find markers (Find markers #4 asap_markers) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/376212/" ## Running Find markers [376212] [Find markers #4 asap_markers] () echo '-> Running Find markers [376212] [Find markers #4 asap_markers] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376212 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -o /data/asap2/users/776/2d1rq4/markers/291057 --iAnnot /col_attrs/_clust_1_seurat --id 2475476 --is_count_table 1> /data/asap2/users/776/k4r829/markers/291057/exec.out 2> /data/asap2/users/776/k4r829/markers/291057/exec.err'" ## ---------------------------------------------------------------- ## Run 376213 Marker enrichment (Marker enrichment #5 asap_marker_enrichment) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/376213/" ## Running Marker enrichment [376213] [Marker enrichment #5 asap_marker_enrichment] () echo '-> Running Marker enrichment [376213] [Marker enrichment #5 asap_marker_enrichment] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_376213 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/776/2d1rq4/markers/291057 -o /data/asap2/users/776/2d1rq4/markers/291058 --genesets 58,60,59,2091,57,2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/k4r829/markers/291058/exec.out 2> /data/asap2/users/776/k4r829/markers/291058/exec.err'" ## ---------------------------------------------------------------- ## Run 416395 Find markers (Find markers #5 asap_markers) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/markers/416395/" ## Running Find markers [416395] [Find markers #5 asap_markers] (input_matrix:gene_filtering #1) echo '-> Running Find markers [416395] [Find markers #5 asap_markers] (input_matrix:gene_filtering #1)' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_416395 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T FindMarkers --loom /data/asap2/users/776/2d1rq4/gene_filtering/376148/output.loom -o /data/asap2/users/776/2d1rq4/markers/416395 --iAnnot /col_attrs/_clust_1_seurat --id 3142605 --is_count_table true 1> /data/asap2/users/776/2d1rq4/markers/416395/exec.out 2> /data/asap2/users/776/2d1rq4/markers/416395/exec.err'" ## ---------------------------------------------------------------- ## Run 416396 Marker enrichment (Marker enrichment #6 asap_marker_enrichment) ## ---------------------------------------------------------------- ## Ensure output directory exists docker run --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "mkdir -p $PROJECT_DIR/marker_enrich/416396/" ## Running Marker enrichment [416396] [Marker enrichment #6 asap_marker_enrichment] () echo '-> Running Marker enrichment [416396] [Marker enrichment #6 asap_marker_enrichment] ()' ## Command docker run -v /data/asap2_test:/data/asap2_test --name asap_dev_416396 --net=host -e HOST_USER_ID=$(id -u) -e HOST_USER_GID=$(id -g) --entrypoint '/bin/sh' --rm -v $ASAP_PROJECTS_DIR:$ASAP_PROJECTS_DIR fabdavid/asap_run:v5 -c "sh -c 'java -jar /srv/ASAP.jar -T MarkerEnrichment -i /data/asap2/users/776/2d1rq4/markers/416395 -o /data/asap2/users/776/2d1rq4/markers/416396 --genesets 3152,58,60,59,2091,57,2769 -h $ASAP_DATA_DB_HOST:$ASAP_DATA_DB_PORT/asap_data_v6 1> /data/asap2/users/776/2d1rq4/markers/416396/exec.out 2> /data/asap2/users/776/2d1rq4/markers/416396/exec.err'"