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Commit 81f03e74 authored by ahb-ufz's avatar ahb-ufz
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stdout for snakemake submit

parent 0285f9db
Pipeline #39770 failed with stages
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              Showing with 23 additions and 21 deletions
              runscripts/IMP3_withReport.sh
              View file @ 81f03e74
              ...@@ -19,9 +19,9 @@ eval $LOADING_MODULES ...@@ -19,9 +19,9 @@ eval $LOADING_MODULES
              eval $CONDA_START eval $CONDA_START
              if [ "$LOCK_SETTINGS" = true ]; then if [ "$LOCK_SETTINGS" = true ]; then
              snakemake --cores $THREADS -s $DIR/Snakefile --keep-going --local-cores 1 --cluster-config $DIR/config/$SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition}" --configfile $CONFIGFILE --config sessionName=$JNAME locked_normalMem=$NORMAL_MEM_EACH locked_bigMem=$BIGMEM_MEM_EACH locked_bigCores=$BIGMEM_CORES locked_bigTotal=$BIGMEM_TOTAL settingsLocked=true sessionKind=cluster --use-conda --conda-prefix $DIR/conda >> $JNAME.stdout 2>> $JNAME.stderr snakemake --cores $THREADS -s $DIR/Snakefile --keep-going --local-cores 1 --cluster-config $DIR/config/$SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition} {cluster.stdout}" --configfile $CONFIGFILE --config sessionName=$JNAME locked_normalMem=$NORMAL_MEM_EACH locked_bigMem=$BIGMEM_MEM_EACH locked_bigCores=$BIGMEM_CORES locked_bigTotal=$BIGMEM_TOTAL settingsLocked=true sessionKind=cluster --use-conda --conda-prefix $DIR/conda >> $JNAME.stdout 2>> $JNAME.stderr
              else else
              snakemake --cores $THREADS -s $DIR/Snakefile --keep-going --local-cores 1 --cluster-config $DIR/config/$SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition}" --configfile $CONFIGFILE --config sessionName=$JNAME sessionKind=cluster --use-conda --conda-prefix $DIR/conda >> $JNAME.stdout 2>> $JNAME.stderr snakemake --cores $THREADS -s $DIR/Snakefile --keep-going --local-cores 1 --cluster-config $DIR/config/$SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition} {cluster.stdout}" --configfile $CONFIGFILE --config sessionName=$JNAME sessionKind=cluster --use-conda --conda-prefix $DIR/conda >> $JNAME.stdout 2>> $JNAME.stderr
              fi fi
              snakemake --cores 1 -s $DIR/Snakefile --report report.html --configfile $CONFIGFILE snakemake --cores 1 -s $DIR/Snakefile --report report.html --configfile $CONFIGFILE
              ......
              runscripts/IMP3_withoutReport.sh
              View file @ 81f03e74
              ...@@ -19,9 +19,9 @@ eval $LOADING_MODULES ...@@ -19,9 +19,9 @@ eval $LOADING_MODULES
              eval $CONDA_START eval $CONDA_START
              if [ "$LOCK_SETTINGS" = true ]; then if [ "$LOCK_SETTINGS" = true ]; then
              snakemake --cores $THREADS -s $DIR/Snakefile --keep-going --local-cores 1 --cluster-config $DIR/config/$SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition}" --configfile $CONFIGFILE --config sessionName=$JNAME locked_normalMem=$NORMAL_MEM_EACH locked_bigMem=$BIGMEM_MEM_EACH locked_bigCores=$BIGMEM_CORES locked_bigTotal=$BIGMEM_TOTAL settingsLocked=true sessionKind=cluster --use-conda --conda-prefix $DIR/conda >> $JNAME.stdout 2>> $JNAME.stderr snakemake --cores $THREADS -s $DIR/Snakefile --keep-going --local-cores 1 --cluster-config $DIR/config/$SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition} {cluster.stdout}" --configfile $CONFIGFILE --config sessionName=$JNAME locked_normalMem=$NORMAL_MEM_EACH locked_bigMem=$BIGMEM_MEM_EACH locked_bigCores=$BIGMEM_CORES locked_bigTotal=$BIGMEM_TOTAL settingsLocked=true sessionKind=cluster --use-conda --conda-prefix $DIR/conda >> $JNAME.stdout 2>> $JNAME.stderr
              else else
              snakemake --cores $THREADS -s $DIR/Snakefile --keep-going --local-cores 1 --cluster-config $DIR/config/$SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition}" --configfile $CONFIGFILE --config sessionName=$JNAME sessionKind=cluster --use-conda --conda-prefix $DIR/conda >> $JNAME.stdout 2>> $JNAME.stderr snakemake --cores $THREADS -s $DIR/Snakefile --keep-going --local-cores 1 --cluster-config $DIR/config/$SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition} {cluster.stdout}" --configfile $CONFIGFILE --config sessionName=$JNAME sessionKind=cluster --use-conda --conda-prefix $DIR/conda >> $JNAME.stdout 2>> $JNAME.stderr
              fi fi
              ......
              runscripts/runIMP3_tmux.sh
              View file @ 81f03e74
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