update to openmpi/4.1.0

Sydney-Informatics-Hub · Jul 8, 2021 · 47ddacf · 47ddacf
1 parent 02bf5f0
commit 47ddacf
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Showing 39 changed files with 34 additions and 45 deletions.
diff --git a/Scripts/align.sh → align.sh b/Scripts/align.sh → align.sh
diff --git a/Scripts/align_make_input.sh → align_make_input.sh b/Scripts/align_make_input.sh → align_make_input.sh
diff --git a/Scripts/align_nonhuman.sh → align_nonhuman.sh b/Scripts/align_nonhuman.sh → align_nonhuman.sh
diff --git a/Scripts/align_run_parallel.pbs → align_run_parallel.pbs b/Scripts/align_run_parallel.pbs → align_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/align.o
 #PBS -e ./Logs/align.e
-#PBS -l storage=
+#PBS -l storage=scratch/public+
 
 set -e
 
@@ -44,8 +44,7 @@ mkdir -p ../Align_split ../HLA_fastq ./Logs/Align ./Logs/Align_error_capture
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load samtools/1.10
 module load bwa/0.7.17
 module load k8/0.2.5
@@ -62,7 +61,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 
diff --git a/Scripts/bqsr_apply.sh → bqsr_apply.sh b/Scripts/bqsr_apply.sh → bqsr_apply.sh
diff --git a/Scripts/bqsr_apply_make_input.sh → bqsr_apply_make_input.sh b/Scripts/bqsr_apply_make_input.sh → bqsr_apply_make_input.sh
diff --git a/Scripts/bqsr_apply_run_parallel.pbs → bqsr_apply_run_parallel.pbs b/Scripts/bqsr_apply_run_parallel.pbs → bqsr_apply_run_parallel.pbs
@@ -32,7 +32,7 @@
 #PBS -l wd
 #PBS -o ./Logs/bqsr_apply.o
 #PBS -e ./Logs/bqsr_apply.e
-#PBS -lstorage=
+#PBS -lstorage=scratch/public+
 
 set -e
 
@@ -45,8 +45,7 @@ mkdir -p ../BQSR_apply ./Logs/BQSR_apply ./Logs/BQSR_apply_error_capture
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load gatk/4.1.8.1 #loads also java/jdk1.8.0_60
 module load samtools/1.10
 
@@ -59,7 +58,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 
diff --git a/Scripts/bqsr_gather.sh → bqsr_gather.sh b/Scripts/bqsr_gather.sh → bqsr_gather.sh
diff --git a/Scripts/bqsr_gather_make_input.sh → bqsr_gather_make_input.sh b/Scripts/bqsr_gather_make_input.sh → bqsr_gather_make_input.sh
diff --git a/Scripts/bqsr_gather_run_parallel.pbs → bqsr_gather_run_parallel.pbs b/Scripts/bqsr_gather_run_parallel.pbs → bqsr_gather_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/bqsr_gather.o
 #PBS -e ./Logs/bqsr_gather.e
-#PBS -lstorage=
+#PBS -lstorage=scratch/public+
 
 set -e
 
@@ -43,8 +43,7 @@ PBS_NCI_NCPUS_PER_NODE=$PBS_NCPUS #Include if requesting less than a full node
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load gatk/4.1.8.1
 
 # SCRIPT
@@ -56,7 +55,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 

diff --git a/Scripts/bqsr_merge.sh → bqsr_merge.sh b/Scripts/bqsr_merge.sh → bqsr_merge.sh
diff --git a/Scripts/bqsr_merge_make_input.sh → bqsr_merge_make_input.sh b/Scripts/bqsr_merge_make_input.sh → bqsr_merge_make_input.sh
diff --git a/Scripts/bqsr_merge_run_parallel.pbs → bqsr_merge_run_parallel.pbs b/Scripts/bqsr_merge_run_parallel.pbs → bqsr_merge_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/bqsr_merge.o
 #PBS -e ./Logs/bqsr_merge.e
-#PBS -lstorage=
+#PBS -lstorage=scratch/public+
 
 set -e
 
@@ -46,8 +46,7 @@ mkdir -p ../Final_bams ./Logs/BQSR_merge ./Logs/BQSR_merge_error_capture
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load gatk/4.1.8.1
 
 # SCRIPT
@@ -59,7 +58,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 
diff --git a/Scripts/bqsr_recal.sh → bqsr_recal.sh b/Scripts/bqsr_recal.sh → bqsr_recal.sh
diff --git a/Scripts/bqsr_recal_make_input.sh → bqsr_recal_make_input.sh b/Scripts/bqsr_recal_make_input.sh → bqsr_recal_make_input.sh
diff --git a/Scripts/bqsr_recal_run_parallel.pbs → bqsr_recal_run_parallel.pbs b/Scripts/bqsr_recal_run_parallel.pbs → bqsr_recal_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/bqsr_recal.o
 #PBS -e ./Logs/bqsr_recal.e
-#PBS -lstorage=
+#PBS -lstorage=scratch/public+
 
 set -e
 
@@ -44,8 +44,7 @@ mkdir -p ../BQSR_tables ./Logs/BQSR_recal ./Logs/BQSR_recal_error_capture
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load gatk/4.1.8.1
 
 # SCRIPT
@@ -57,7 +56,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 
diff --git a/Scripts/bwa-postalt.js → bwa-postalt.js b/Scripts/bwa-postalt.js → bwa-postalt.js
diff --git a/Scripts/create_gatk_ref_intervals.pbs → create_gatk_ref_intervals.pbs b/Scripts/create_gatk_ref_intervals.pbs → create_gatk_ref_intervals.pbs
@@ -33,7 +33,7 @@
 #PBS -l wd
 #PBS -o ./Logs/gatk_ref_intervals.o
 #PBS -e ./Logs/gatk_ref_intervals.e
-#PBS -lstorage=
+#PBS -lstorage=scratch/public+
 
 module load gatk/4.1.8.1
 

diff --git a/create_project.bash b/create_project.bash
diff --git a/Scripts/dedup_sort.sh → dedup_sort.sh b/Scripts/dedup_sort.sh → dedup_sort.sh
diff --git a/Scripts/dedup_sort_make_input.sh → dedup_sort_make_input.sh b/Scripts/dedup_sort_make_input.sh → dedup_sort_make_input.sh
diff --git a/Scripts/dedup_sort_run_parallel.pbs → dedup_sort_run_parallel.pbs b/Scripts/dedup_sort_run_parallel.pbs → dedup_sort_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/dedup_sort.o
 #PBS -e ./Logs/dedup_sort.e
-#PBS -l storage=
+#PBS -l storage=scratch/public+
 
 set -e
 
@@ -45,8 +45,7 @@ mkdir -p ../Dedup_sort ../SplitDisc ./Logs/Dedup_sort ./Logs/Dedup_sort_error_ca
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load samtools/1.10
 samblaster=/scratch/er01/apps/samblaster/0.1.24/samblaster
 
@@ -59,7 +58,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 
diff --git a/Scripts/fastqc.sh → fastqc.sh b/Scripts/fastqc.sh → fastqc.sh
diff --git a/Scripts/fastqc_make_input.sh → fastqc_make_input.sh b/Scripts/fastqc_make_input.sh → fastqc_make_input.sh
diff --git a/Scripts/fastqc_run_parallel.pbs → fastqc_run_parallel.pbs b/Scripts/fastqc_run_parallel.pbs → fastqc_run_parallel.pbs
@@ -29,7 +29,7 @@
 #PBS -l wd
 #PBS -q normalbw
 #PBS -W umask=022
-#PBS -l storage=
+#PBS -l storage=scratch/public+
 #PBS -o ./Logs/fastqc.o
 #PBS -e ./Logs/fastqc.e
 
@@ -46,8 +46,7 @@ PBS_NCI_NCPUS_PER_NODE=$PBS_NCPUS
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load fastqc/0.11.7
 
 # SCRIPT
@@ -59,6 +58,6 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
diff --git a/Scripts/index.sh → index.sh b/Scripts/index.sh → index.sh
diff --git a/Scripts/index_make_input.sh → index_make_input.sh b/Scripts/index_make_input.sh → index_make_input.sh
diff --git a/Scripts/index_reference.pbs → index_reference.pbs b/Scripts/index_reference.pbs → index_reference.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/index_ref.o
 #PBS -e ./Logs/index_ref.e
-#PBS -lstorage=
+#PBS -lstorage=scratch/public+
 
 
 module load bwa/0.7.17

diff --git a/Scripts/index_run_parallel.pbs → index_run_parallel.pbs b/Scripts/index_run_parallel.pbs → index_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/index.o
 #PBS -e ./Logs/index.e
-#PBS -l storage=
+#PBS -l storage=scratch/public+
 
 set -e
 
@@ -43,8 +43,7 @@ NCPUS=24
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load samtools/1.10
 
 # SCRIPT
@@ -56,7 +55,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 
diff --git a/Scripts/merge_align.sh → merge_align.sh b/Scripts/merge_align.sh → merge_align.sh
diff --git a/..._check_fastq_input_vs_bam_output_sizes.sh → ..._check_fastq_input_vs_bam_output_sizes.sh b/..._check_fastq_input_vs_bam_output_sizes.sh → ..._check_fastq_input_vs_bam_output_sizes.sh
diff --git a/Scripts/merge_align_make_input.sh → merge_align_make_input.sh b/Scripts/merge_align_make_input.sh → merge_align_make_input.sh
diff --git a/Scripts/merge_align_run_parallel.pbs → merge_align_run_parallel.pbs b/Scripts/merge_align_run_parallel.pbs → merge_align_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/merge_align.o
 #PBS -e ./Logs/merge_align.e
-#PBS -l storage=
+#PBS -l storage=scratch/public+
 
 set -e
 
@@ -48,8 +48,7 @@ mkdir -p ../Merge_align ./Logs/Merge_align_error_capture
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load sambamba/0.7.1
 module load samtools/1.10
 
@@ -62,7 +61,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 
diff --git a/Scripts/split_fastq.sh → split_fastq.sh b/Scripts/split_fastq.sh → split_fastq.sh
diff --git a/...astq_check_fastq_input_vs_split_output.sh → ...astq_check_fastq_input_vs_split_output.sh b/...astq_check_fastq_input_vs_split_output.sh → ...astq_check_fastq_input_vs_split_output.sh
diff --git a/...tq_input_vs_split_output_run_parallel.pbs → ...tq_input_vs_split_output_run_parallel.pbs b/...tq_input_vs_split_output_run_parallel.pbs → ...tq_input_vs_split_output_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/check_split_fastq.o
 #PBS -e ./Logs/check_split_fastq.e
-#PBS -l storage=
+#PBS -l storage=scratch/public+
 
 # For singleton data:
 #SCRIPT=./Scripts/split_fastq_singletons.sh
@@ -47,8 +47,7 @@ mkdir -p ../Check_split_fastq
 # Do not edit below this line
 #########################################################
 
-module load openmpi/4.0.2
-module load nci-parallel/1.0.0
+module load openmpi/4.1.0
 module load parallel/20191022
 
 SCRIPT=./split_fastq_check_fastq_input_vs_split_output.sh
@@ -59,7 +58,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file
 
diff --git a/...fastq_input_vs_split_output_singletons.sh → ...fastq_input_vs_split_output_singletons.sh b/...fastq_input_vs_split_output_singletons.sh → ...fastq_input_vs_split_output_singletons.sh
diff --git a/Scripts/split_fastq_make_input.sh → split_fastq_make_input.sh b/Scripts/split_fastq_make_input.sh → split_fastq_make_input.sh
diff --git a/Scripts/split_fastq_run_parallel.pbs → split_fastq_run_parallel.pbs b/Scripts/split_fastq_run_parallel.pbs → split_fastq_run_parallel.pbs
@@ -31,7 +31,7 @@
 #PBS -l wd
 #PBS -o ./Logs/split_fastq.o
 #PBS -e ./Logs/split_fastq.e
-#PBS -l storage=
+#PBS -l storage=scratch/public+
 
 INPUTS=./Inputs/split_fastq.inputs
 # NCPUS per task
@@ -43,7 +43,6 @@ mkdir -p ../Split_fastq ./Logs/split_fastq
 # Do not edit below this line
 #########################################################
 
-module load nci-parallel/1.0.0
 module load fastp/0.20.0
 
 SCRIPT=./split_fastq.sh
@@ -54,7 +53,7 @@ sed "s|^|${SCRIPT} |" ${INPUTS} > ${PBS_JOBFS}/input-file
 
 mpirun --np $((M * PBS_NCPUS / PBS_NCI_NCPUS_PER_NODE)) \
         --map-by node:PE=${NCPUS} \
-        nci-parallel \
+        /scratch/public/bjm900/nci-parallel/bin/nci-parallel \
         --verbose \
         --input-file ${PBS_JOBFS}/input-file