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Update LaunchMetrics.py
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increasing the bin memory for dragen.  dragen command is failing analysis on an Amplicon project
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@darrelln32
darrelln32 committed Jan 20, 2025
1 parent fb4edbf commit 24a1eab
Showing 1 changed file with 6 additions and 6 deletions.
12 changes: 6 additions & 6 deletions scripts/LaunchMetrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -149,8 +149,8 @@ def dragen_rna_alignment_and_metrics(sample, run, sample_parameters, rna_directo
rna_dragen_job_name_header = "{}___RNA_DRAGEN___".format(run)


launch_dragen_rna = "/opt/edico/bin/dragen -f -r {} --fastq-list {} --fastq-list-sample-id {} -a {} --intermediate-results-dir /staging/temp --enable-map-align true --enable-sort true --enable-bam-indexing true --enable-map-align-output true --output-format BAM --enable-rna true --enable-duplicate-marking true --enable-rna-quantification true --output-file-prefix {} --output-directory {} --bin_memory 50000000000".format(rna_path, fastq_list, sample.sample_id, sample_parameters["GTF"], sample.sample_id, rna_directory)
bsub_launch_dragen_rna = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 48 -M 4 {3}".format(rna_dragen_job_name_header, sample.sample_id, rna_directory, launch_dragen_rna)
launch_dragen_rna = "/opt/edico/bin/dragen -f -r {} --fastq-list {} --fastq-list-sample-id {} -a {} --intermediate-results-dir /staging/temp --enable-map-align true --enable-sort true --enable-bam-indexing true --enable-map-align-output true --output-format BAM --enable-rna true --enable-duplicate-marking true --enable-rna-quantification true --output-file-prefix {} --output-directory {} --bin_memory 75000000000".format(rna_path, fastq_list, sample.sample_id, sample_parameters["GTF"], sample.sample_id, rna_directory)
bsub_launch_dragen_rna = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 50 -M 4 {3}".format(rna_dragen_job_name_header, sample.sample_id, rna_directory, launch_dragen_rna)
print(bsub_launch_dragen_rna)
call(bsub_launch_dragen_rna, shell = True)

Expand Down Expand Up @@ -186,8 +186,8 @@ def dragen(sample, run, sample_parameters, work_directory, dragen_directory, fas
vcfFileOption = ""

metric_file_prefix = "{}___P{}___{}___{}".format(run, sample.project[8:], sample.sample_id, sample_parameters["GTAG"])
launch_dragen = "/opt/edico/bin/dragen --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true --bin_memory 50000000000 {}".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id, vcfFileOption)
bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 48 -M 4 {3}".format(dragen_job_name_header, sample.sample_id, dragen_directory, launch_dragen)
launch_dragen = "/opt/edico/bin/dragen --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true --bin_memory 75000000000 {}".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id, vcfFileOption)
bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 50 -M 4 {3}".format(dragen_job_name_header, sample.sample_id, dragen_directory, launch_dragen)
print(bsub_launch_dragen)
call(bsub_launch_dragen, shell = True)

Expand Down Expand Up @@ -229,8 +229,8 @@ def dragen_methylation(sample, run, sample_parameters, work_directory, dragen_di
dragen_path = "/igo/work/igo/dragen_hash_tables/4.2/grcm39_methylated"

metric_file_prefix = "{}___P{}___{}___{}".format(run, sample.project[8:], sample.sample_id, sample_parameters["GTAG"])
launch_dragen_methylation = "/opt/edico/bin/dragen --enable-methylation-calling true --methylation-protocol directional --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true --bin_memory 50000000000".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id)
bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 48 -M 4 {3}".format(dragen_methylation_job_name_header, sample.sample_id, dragen_directory, launch_dragen_methylation)
launch_dragen_methylation = "/opt/edico/bin/dragen --enable-methylation-calling true --methylation-protocol directional --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true --bin_memory 75000000000".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id)
bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 50 -M 4 {3}".format(dragen_methylation_job_name_header, sample.sample_id, dragen_directory, launch_dragen_methylation)
print(bsub_launch_dragen)
call(bsub_launch_dragen, shell = True)

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