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gatk variantrecalibrator wrapper does not specify properly the resources path #280

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alejocrojo09 opened this issue Jan 12, 2021 · 1 comment
Open

gatk variantrecalibrator wrapper does not specify properly the resources path #280

alejocrojo09 opened this issue Jan 12, 2021 · 1 comment
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@alejocrojo09
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alejocrojo09 commented Jan 12, 2021 •
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Snakemake version
Snakemake v5.31.1
Wrapper 0.68.0/bio/gatk/variantrecalibrator

Describe the bug
For VariantRecalibrator, I have my own path for the vcf files of the resources. When running the rule, I get an error from GATK that the resource does not exist. Checking the wrapper's code, it seems that there is a syntax error when returning the resources path. For GATK v4.1.1, the ":" in the parameters is removed according to:
https://gatk.broadinstitute.org/hc/en-us/community/posts/360072126112-Variant-Recalibrator-Couldn-t-read-file

Logs
Snakemake
RuleException:
CalledProcessError in line 52 of /home/VITO/correara/genomics/rules/filtering.smk:
Command 'source /home/VITO/correara/miniconda3/bin/activate '/home/VITO/correara/genomics/.snakemake/conda/d509627e'; set -euo pipefail; python /home/VITO/correara/genomics/.snakemake/scripts/tmpz9cha92t.wrapper.py' returned non-zero exit status 1.
File "/home/VITO/correara/miniconda3/envs/BioSnake/lib/python3.9/site-packages/snakemake/executors/init.py", line 2317, in run_wrapper
File "/home/VITO/correara/genomics/rules/filtering.smk", line 52, in __rule_recalibrate_calls
File "/home/VITO/correara/miniconda3/envs/BioSnake/lib/python3.9/site-packages/snakemake/executors/init.py", line 566, in _callback
File "/home/VITO/correara/miniconda3/envs/BioSnake/lib/python3.9/concurrent/futures/thread.py", line 52, in run
File "/home/VITO/correara/miniconda3/envs/BioSnake/lib/python3.9/site-packages/snakemake/executors/init.py", line 552, in cached_or_run
File "/home/VITO/correara/miniconda3/envs/BioSnake/lib/python3.9/site-packages/snakemake/executors/init.py", line 2348, in run_wrapper

GATK
Using GATK jar /home/VITO/correara/genomics/.snakemake/conda/d509627e/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/VITO/correara/genomics/.snakemake/conda/d509627e/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar VariantRecalibrator --max-gaussians 4 --resource hapmap,known=false,training=true,truth=true,prior=15.0:/home/VITO/correara/genomics/hapmap/hapmap_3.3.hg38.vcf.gz --resource omni,known=false,training=true,truth=false,prior=12.0:/home/VITO/correara/genomics/omni/1000G_omni2.5.hg38.vcf.gz --resource g1k,known=false,training=true,truth=false,prior=10.0:/home/VITO/correara/genomics/g1k/1000G_phase1.snps.high_confidence.hg38.vcf.gz --resource dbsnp,known=true,training=false,truth=false,prior=2.0:/home/VITO/correara/genomics/dbsnp/hg38_dbsnp138.vcf.gz -R resources/hg38/hg38.fa -V filtered/ERR032031.indels.vcf.gz -mode INDEL --output filtered/ERR032031.indels.recalibrated.vcf.gz --tranches-file filtered/ERR032031.indels.tranches -an QD -an FS -an ReadPosRankSum -an MQRankSum -an SOR -an DP
13:58:07.143 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/VITO/correara/genomics/.snakemake/conda/d509627e/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jan 09, 2021 1:58:07 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:58:07.421 INFO VariantRecalibrator - ------------------------------------------------------------
13:58:07.421 INFO VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.4.1
13:58:07.422 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
13:58:07.422 INFO VariantRecalibrator - Executing as correara@dev01 on Linux v4.4.0-198-generic amd64
13:58:07.422 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-b11
13:58:07.422 INFO VariantRecalibrator - Start Date/Time: January 9, 2021 1:58:07 PM CET
13:58:07.422 INFO VariantRecalibrator - ------------------------------------------------------------
13:58:07.422 INFO VariantRecalibrator - ------------------------------------------------------------
13:58:07.422 INFO VariantRecalibrator - HTSJDK Version: 2.21.0
13:58:07.422 INFO VariantRecalibrator - Picard Version: 2.21.2
13:58:07.422 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:58:07.422 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:58:07.422 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:58:07.423 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:58:07.423 INFO VariantRecalibrator - Deflater: IntelDeflater
13:58:07.423 INFO VariantRecalibrator - Inflater: IntelInflater
13:58:07.423 INFO VariantRecalibrator - GCS max retries/reopens: 20
13:58:07.423 INFO VariantRecalibrator - Requester pays: disabled
13:58:07.423 INFO VariantRecalibrator - Initializing engine
13:58:08.124 INFO VariantRecalibrator - Shutting down engine
[January 9, 2021 1:58:08 PM CET] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=627572736

A USER ERROR has occurred: Couldn't read file file:///home/VITO/correara/genomics/hapmap,known=false,training=true,truth=true,prior=15.0:/home/VITO/correara/genomics/hapmap/hapmap_3.3.hg38.vcf.gz. Error was: It doesn't exist.

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Minimal example

rule recalibrate_calls:
      input:
          vcf = "filtered/{sample}.{vartype}.vcf.gz",
          ref = "resources/hg38/hg38.fa",
          hapmap = "/home/VITO/correara/genomics/hapmap/hapmap_3.3.hg38.vcf.gz",
          omni = "/home/VITO/correara/genomics/omni/1000G_omni2.5.hg38.vcf.gz",
          g1k = "/home/VITO/correara/genomics/g1k/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
          dbsnp = "/home/VITO/correara/genomics/dbsnp/hg38_dbsnp138.vcf.gz",
      output:
          vcf = temp("filtered/{sample}.{vartype}.recalibrated.vcf.gz"),
          tranches = "filtered/{sample}.{vartype}.tranches",
          rscript = "filtered/{sample}.{vartype}.recal.plots.R"
      params:
          mode = get_mode,
          resources = {"hapmap": {"known": False, "training": True, "truth": True, "prior": 15.0},
                   "omni":   {"known": False, "training": True, "truth": False, "prior": 12.0},
                   "g1k":   {"known": False, "training": True, "truth": False, "prior": 10.0},
                   "dbsnp":  {"known": True, "training": False, "truth": False, "prior": 2.0}},
          annotation = ["QD", "FS", "ReadPosRankSum", "MQRankSum", "SOR", "DP"],
          extra = get_gaussians
      log:
          "logs/gatk.{sample}.{vartype}.variantrecalibrator.log"
      wrapper:
          "0.68.0/bio/gatk/variantrecalibrator"

Could it be possible to fix the wrapper with the updated GATK syntax?
@alejocrojo09 alejocrojo09 added the bug Something isn't working label Jan 12, 2021
@fgvieira
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fgvieira commented Mar 2, 2022

GATK wrappers were all recently updated. Can you check if the error still persists?

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