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The first running Funcotator is stucked #5903

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JavisPeng opened this issue Apr 24, 2019 · 7 comments
Closed

The first running Funcotator is stucked #5903

JavisPeng opened this issue Apr 24, 2019 · 7 comments
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@jonn-smith
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Funcotator

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@JavisPeng
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JavisPeng commented Apr 24, 2019 •
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ENV: Centos7 JAVA1.8 GTAK4.1.0.0
Preparation:

  1. download datasource funcotator_dataSources.v1.6.20190124g
  2. untar the gnomAD
fa=/share/share/data/NGS/ref_index/GATK_bundle/hg38/Homo_sapiens_assembly38.fasta
func=/share/share/data/NGS/ref_index/GATK_bundle/funcotator_dataSources.v1.6.20190124g
gatk Funcotator \
	--variant ../relapse.filtered.snps.indels.vcf \
	--reference $fa \
	--ref-version hg38 \
	--data-sources-path $func \
	--output relapse.funcotated.maf \
	--output-file-format MAF

after running the script above, it stucked and show nothing anymore, is there something I ignored ?

Using GATK jar /share/share/soft/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /share/share/soft/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar Funcotator --variant ../relapse.filtered.snps.indels.vcf --reference /share/share/data/NGS/ref_index/GATK_bundle/hg38/Homo_sapiens_assembly38.fasta --ref-version hg38 --data-sources-path /share/share/data/NGS/ref_index/GATK_bundle/funcotator_dataSources.v1.6.20190124g --output relapse.funcotated.maf --output-file-format MAF
10:24:47.787 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/share/soft/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:24:50.558 INFO  Funcotator - ------------------------------------------------------------
10:24:50.559 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.1.0.0
10:24:50.559 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
10:24:50.560 INFO  Funcotator - Executing as javis@node4 on Linux v3.10.0-514.el7.x86_64 amd64
10:24:50.560 INFO  Funcotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_161-b12
10:24:50.560 INFO  Funcotator - Start Date/Time: April 24, 2019 10:24:47 AM CST
10:24:50.560 INFO  Funcotator - ------------------------------------------------------------
10:24:50.560 INFO  Funcotator - ------------------------------------------------------------
10:24:50.561 INFO  Funcotator - HTSJDK Version: 2.18.2
10:24:50.561 INFO  Funcotator - Picard Version: 2.18.25
10:24:50.561 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:24:50.561 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:24:50.562 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:24:50.562 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:24:50.562 INFO  Funcotator - Deflater: IntelDeflater
10:24:50.562 INFO  Funcotator - Inflater: IntelInflater
10:24:50.562 INFO  Funcotator - GCS max retries/reopens: 20
10:24:50.562 INFO  Funcotator - Requester pays: disabled
10:24:50.562 INFO  Funcotator - Initializing engine
10:24:51.150 INFO  FeatureManager - Using codec VCFCodec to read file file:///sdb/research_th/Exon_Seq/2_classes/joint_out/relapse_joint/t_func/../relapse.filtered.snps.indels.vcf
10:24:51.387 INFO  Funcotator - Done initializing engine
10:24:51.387 INFO  Funcotator - Validating Sequence Dictionaries...
10:24:51.422 INFO  Funcotator - Processing user transcripts/defaults/overrides...
10:24:51.423 INFO  Funcotator - Initializing data sources...
10:24:51.425 INFO  DataSourceUtils - Initializing data sources from directory: /share/share/data/NGS/ref_index/GATK_bundle/funcotator_dataSources.v1.6.20190124g
10:24:51.427 INFO  DataSourceUtils - Data sources version: 1.6.2019124g
10:24:51.427 INFO  DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz
10:24:51.427 INFO  DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz
10:24:51.436 INFO  DataSourceUtils - Resolved data source file path: file:///sdb/research_th/Exon_Seq/2_classes/joint_out/relapse_joint/t_func/clinvar_20180429_hg38.vcf -> file:///share/share/data/NGS/ref_index/GATK_bundle/funcotator_dataSources.v1.6.20190124g/clinvar/hg38/clinvar_20180429_hg38.vcf
10:24:51.439 INFO  DataSourceUtils - Resolved data source file path: file:///sdb/research_th/Exon_Seq/2_classes/joint_out/relapse_joint/t_func/acmg_lof.tsv -> file:///share/share/data/NGS/ref_index/GATK_bundle/funcotator_dataSources.v1.6.20190124g/acmg_lof/hg38/acmg_lof.tsv
10:24:51.442 INFO  DataSourceUtils - Resolved data source file path: file:///sdb/research_th/Exon_Seq/2_classes/joint_out/relapse_joint/t_func/acmg59_test_cleaned.txt -> file:///share/share/data/NGS/ref_index/GATK_bundle/funcotator_dataSources.v1.6.20190124g/acmg_rec/hg38/acmg59_test_cleaned.txt
10:24:51.444 INFO  DataSourceUtils - Resolved data source file path: file:///sdb/research_th/Exon_Seq/2_classes/joint_out/relapse_joint/t_func/gencode.v27.chr_patch_hapl_scaff.annotation.REORDERED.gtf -> file:///share/share/data/NGS/ref_index/GATK_bundle/funcotator_dataSources.v1.6.20190124g/gencode/hg38/gencode.v27.chr_patch_hapl_scaff.annotation.REORDERED.gtf
10:24:51.445 INFO  DataSourceUtils - Resolved data source file path: file:///sdb/research_th/Exon_Seq/2_classes/joint_out/relapse_joint/t_func/gencode.v27.transcripts.fasta -> file:///share/share/data/NGS/ref_index/GATK_bundle/funcotator_dataSources.v1.6.20190124g/gencode/hg38/gencode.v27.transcripts.fasta
@droazen
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droazen commented Apr 24, 2019

@JavisPeng Does the tool still hang if you don't untar gnomAD?

@jonn-smith
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@JavisPeng I think it is having trouble connecting to google cloud to get the gnomAD data.

As an alternative you can download the gnomAD data directly to your machine and run against a local copy.

@jonn-smith
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@JavisPeng I wanted to check in. Did you have a chance to download gnomAD locally and run from that? If not, I think that will fix the issue you're seeing. If so, are you all set now?

@JavisPeng
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JavisPeng commented Jul 12, 2019 •
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@droazen Weird，it becomes normal if i don't untar gnomAd

@JavisPeng
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@jonn-smith I have downloaded the gnomAD，it becomes normal if i don't untar gnomAD

@jonn-smith
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Funcotator is trying to read gnomAD from a Google Bucket if the gnomAD data sources are enabled. If you cannot connect to google it will hang. This is ultimately due to the size of the gnomAD data source.

If you can download a local copy and modify the data sources to point to that local copy of gnomAD it will work just fine without an internet connection.

@sainadfensi
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Funcotator is trying to read gnomAD from a Google Bucket if the gnomAD data sources are enabled. If you cannot connect to google it will hang. This is ultimately due to the size of the gnomAD data source.

If you can download a local copy and modify the data sources to point to that local copy of gnomAD it will work just fine without an internet connection.

Hi Jonn,

I have encountered the similar issue. As posted above, the data sources are downloaded and being specified with --data-sources-path $func but still the tool is trying to get online data

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@droazen @jonn-smith @sainadfensi @JavisPeng