I’d like to do find somatic mutations with the UKB WES data using the Mutectcaller (Parabricks accelerated) on UK Biobank Research Analysis Platform. Before I started analysis, I selected a bed file as interval file. The bed file contains just specific genes. The aim of adding the bed file is to filter WES data according to spesific genes. I’m intereted in spesific genes not all genes. So, I’d like to get a small size VCF file end of the analysis. But I received an error which said the interval file is not found when running Mutectcaller. The log was showing below. Please help me to solve this problem. Thank you.
View log of failed sub-job
Logging initialized (priority)
Logging initialized (bulk)
Downloading bundled file parabricks_gpu_asset.tar.gz
Unpacking parabricks_gpu_asset.tar.gz to /
tar: Removing leading/' from member names tar: Removing leading/’ from hard link targets
dxpy/0.355.0 (Linux-5.15.0-1031-aws-x86_64-with-glibc2.29) Python/3.8.10
00:1b.0 3D controller: NVIDIA Corporation TU104GL [Tesla T4] (rev a1)
00:1c.0 3D controller: NVIDIA Corporation TU104GL [Tesla T4] (rev a1)
00:1d.0 3D controller: NVIDIA Corporation TU104GL [Tesla T4] (rev a1)
00:1e.0 3D controller: NVIDIA Corporation TU104GL [Tesla T4] (rev a1)
bash running (job ID job-GYgKy0QJ9Bgzf66ZgX1GQZfv)
Value of ref: ‘{“$dnanexus_link”: “file-GYX8060J6G92G2g63fVGFK0b”}’
Value of in_tumor_bam: ‘{“$dnanexus_link”: “file-GYK8xF0J0X9XBYyv7z50bvJj”}’
Value of tumor_name: ‘UKB_5224901_236244358’
Value of in_tumor_recal_file: ‘’
Value of in_normal_bam: ‘’
Value of normal_name: ‘’
Value of in_normal_recal_file: ‘’
Value of interval_file: ‘{“$dnanexus_link”: “file-GYZ6J4QJ9Bgkj3Z154V92gYj”}’
Value of interval: ‘’
Value of interval_padding: ‘’
Value of ploidy: ‘’
Value of max_mnp_distance: ‘’
Value of mutectcaller_options: ‘’
Docker version 23.0.6, build ef23cbc
Wed Aug 30 07:31:45 2023
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| NVIDIA-SMI 470.129.06 Driver Version: 470.129.06 CUDA Version: 11.4 |
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| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 Tesla T4 Off | 00000000:00:1B.0 Off | 0 |
| N/A 29C P8 9W / 70W | 0MiB / 15109MiB | 0% Default |
| | | N/A |
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| 1 Tesla T4 Off | 00000000:00:1C.0 Off | 0 |
| N/A 28C P8 9W / 70W | 0MiB / 15109MiB | 0% Default |
| | | N/A |
±------------------------------±---------------------±---------------------+
| 2 Tesla T4 Off | 00000000:00:1D.0 Off | 0 |
| N/A 28C P8 9W / 70W | 0MiB / 15109MiB | 0% Default |
| | | N/A |
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| 3 Tesla T4 Off | 00000000:00:1E.0 Off | 0 |
| N/A 28C P8 9W / 70W | 0MiB / 15109MiB | 0% Default |
| | | N/A |
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| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
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| No running processes found |
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00:01.3 Non-VGA unclassified device: Intel Corporation 82371AB/EB/MB PIIX4 ACPI (rev 08)
00:03.0 VGA compatible controller: Amazon.com, Inc. Device 1111
Loaded image: nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1.dnanexus
CHECKING PARABRICKS INSTALL
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation
usage: pbrun []
Help: pbrun -h
command can be a TOOL or FULL PIPELINE. Example:
pbrun fq2bam --ref genome.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam sample.bam
pbrun germline --ref genome.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam sample.bam --out-variants sample.vcf
command options for standalone TOOL
applybqsr - Apply BQSR report to a BAM file and generate a new BAM file
bam2fq - Convert a BAM file to FASTQ
bammetrics - Collect WGS Metrics on a BAM file
bamsort - Sort a BAM file
bqsr - Collect BQSR report on a BAM file
collectmultiplemetrics - Collect multiple classes of metrics on a BAM file
dbsnp - Annotate variants based on a dbsnp
deepvariant - Run GPU-DeepVariant for calling germline variants
fq2bam - Run bwa mem, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration
genotypegvcf - Convert a GVCF to VCF
haplotypecaller - Run GPU-HaplotypeCaller for calling germline variants
indexgvcf - Index a GVCF file
mutectcaller - Run GPU-Mutect2 for tumor-normal analysis
postpon - Generate the final VCF output of doing mutect pon
prepon - Build an index for PON file, which is the prerequisite to performing mutect pon
rna_fq2bam - Run RNA-seq data through the fq2bam pipeline
starfusion - Identify candidate fusion transcripts supported by Illumina reads
command options for commonly used FULL PIPELINES
germline - Run the germline pipeline from FASTQ to VCF
deepvariant_germline - Run the germline pipeline from FASTQ to VCF using a deep neural network analysis
somatic - Run the somatic pipeline from FASTQ to VCF
Information about the software
version - Current version of Parabricks
positional arguments:
command The pipeline or tool to run.
optional arguments:
-h, --help show this help message and exit
input_options: --tumor-name UKB_5224901_236244358 --in-tumor-bam in_tumor_bam.bam
Homo_sapiens_assembly38.dict
Homo_sapiens_assembly38.fasta
Homo_sapiens_assembly38.fasta.amb
Homo_sapiens_assembly38.fasta.ann
Homo_sapiens_assembly38.fasta.bwt
Homo_sapiens_assembly38.fasta.fai
Homo_sapiens_assembly38.fasta.pac
Homo_sapiens_assembly38.fasta.sa
Homo_sapiens_assembly38.known_indels.vcf.gz
Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
Found reference file in bam-index.tar.gz package…
interval_file_options: --interval-file {“$dnanexus_link”: “file-GYZ6J4QJ9Bgkj3Z154V92gYj”}[0].{“$dnanexus_link”: “file-GYZ6J4QJ9Bgkj3Z154V92gYj”}[0]
mutectcaller_options_flags:
Starting pbrun command
[Parabricks Options Error]: Input file {“$dnanexus_link”: not found. Exiting…
[Parabricks Options Error]: Run with -h to see help
END_LOG