CreateSomaticPanelOfNormals (BETA) workflow
REQUIRED for all errors and issues:
a) GATK version used: v.4.4.0
b) Exact command used:
srun apptainer exec $GATK gatk GenomicsDBImport -R /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/PauloM_Analysis/Genome/GRCm39.primary_assembly.genome.fa -L /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/wes/sorted_interval.bed \ --genomicsdb-workspace-path /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/pon_db \
-V /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/CD19CTRL_TZTD190101874_HWYTFCCXY_L2_1_val_1_poni.vcf.gz \
-V /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/SJMMBALL055295_G1-12938-BM-CTRL_R1_val_1_poni.vcf.gz \
-V /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/SJMMBALL055296_G1-13371-BM-CTRL_R1_val_1_poni.vcf.gz \
-V /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/SJMMBALL055297_G1-13286-BM-CTRL_R1_val_1_poni.vcf.gz \
-V /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/SJMMBALL055298_G1-12830-BM-CTRL_R1_val_1_poni.vcf.gz \
-V /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/SJMMBALL055299_G1-12944-BM-CTRL_R1_val_1_poni.vcf.gz \
-V /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/SJMMBALL055300_G1-12942-BM-CTRL_R1_val_1_poni.vcf.gz
#Create pon
srun apptainer exec $GATK gatk CreateSomaticPanelOfNormals -R /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/PauloM_Analysis/Geno> -V gendb:///mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/pon_db \
-O /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/Mutect2/pon.vcf.gz
c) Entire program log:
13:43:21.092 INFO GenomicsDBImport - Importing batch 1 with 7 samples
13:43:23.224 INFO GenomicsDBImport - Importing batch 1 with 7 samples
13:43:25.577 INFO GenomicsDBImport - Importing batch 1 with 7 samples
13:43:27.805 INFO GenomicsDBImport - Importing batch 1 with 7 samples
13:43:30.176 INFO GenomicsDBImport - Importing batch 1 with 7 samples
terminate called after throwing an instance of 'GenomicsDBConfigException'
what(): GenomicsDBConfigException : Syntax error in JSON file /tmp/loader_8690011069316831213.json
Using GATK jar /gatk/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tr>srun: error: compute-3: task 0: Exited with exit code 250
srun: launch/slurm: _step_signal: Terminating StepId=2982450.0
It appears this error on the command of genomicsDBimport
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This tool has been used by our team under Terra premises to generate a PoN using very large number of samples with a custom wdl script that can handle all the forseeable edge cases during this process. It may not be easy for any user to perform this task and as we mentioned before it may not be necessary for you to generate a PoN when you are using inbred model organisms.
I hope this helps.
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