alexcoppe
commented
1 month ago Hi Wan,
Sorry for my late reply. Yes, the issue appears to be related to GATK3. Did you run the pipeline after a stop? I have never encountered this error before.
Let me know.
Alessandro
On Wed, Jul 17, 2024 at 5:04 AM WandaWanda @.***> wrote:
Hi， I am writing to seek your assistance with an issue I have encountered while using the iWhale pipeline. It is a highly efficient tool, and I appreciate its capability to manage reanalysis seamlessly from the point of failure. However, I have encountered an error, the details of which are as follows:
scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: building VCF/Combined_VCFs_by_sample/T_N_merged_indels.vcf' because it doesn't exist java -Xmx4g -jar /tmp/gatk3/GenomeAnalysisTK.jar -T CombineVariants -R /annotations/GRCh38.fa --variant:mutect2 /working/VCF/T_N_mutect2_indels.vcf --variant:strelka2 /working/VCF/T_N_strelka2_indels.vcf --variant:varscan /working/VCF/T_N_varscan_indels.vcf -o VCF/Combined_VCFs_by_sample/T_N_merged_indels.vcf -genotypeMergeOptions PRIORITIZE -priority mutect2,strelka2,varscan INFO 09:37:42,411 HelpFormatter -
INFO 09:37:42,412 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50 INFO 09:37:42,413 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 09:37:42,413 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 09:37:42,413 HelpFormatter - [Tue Jul 16 09:37:42 UTC 2024] Executing on Linux 6.5.0-41-generic amd64 INFO 09:37:42,413 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_161-b12 INFO 09:37:42,416 HelpFormatter - Program Args: -T CombineVariants -R /annotations/GRCh38.fa --variant:mutect2 /working/VCF/T_N_mutect2_indels.vcf --variant:strelka2 /working/VCF/T_N_strelka2_indels.vcf --variant:varscan /working/VCF/T_N_varscan_indels.vcf -o VCF/Combined_VCFs_by_sample/T_N_merged_indels.vcf -genotypeMergeOptions PRIORITIZE -priority mutect2,strelka2,varscan INFO 09:37:42,418 HelpFormatter - Executing as @.*** on Linux 6.5.0-41-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_161-b12. INFO 09:37:42,419 HelpFormatter - Date/Time: 2024/07/16 09:37:42 INFO 09:37:42,419 HelpFormatter -
INFO 09:37:42,419 HelpFormatter -
ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef): ERROR ERROR This means that one or more arguments or inputs in your command are incorrect. ERROR The error message below tells you what is the problem. ERROR ERROR If the problem is an invalid argument, please check the online documentation guide ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ERROR ERROR Visit our website and forum for extensive documentation and answers to ERROR commonly asked questions https://software.broadinstitute.org/gatk ERROR ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ERROR ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file '/working/VCF/T_N_mutect2_indels.vcf' could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types: ERROR Name FeatureType Documentation ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK) ERROR VCF VariantContext (this is an external codec and is not documented within GATK) ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK) ERROR
scons: *** [VCF/Combined_VCFs_by_sample/T_N_merged_indels.vcf] Error 1 scons: building terminated because of errors. `
From my preliminary investigation, it appears that the issue might be related to GATK3 not recognizing the VCF file. I am not sure how to modify the command in docker pipeline. I would greatly appreciate it if you could provide some guidance on how to resolve this matter.
BR, Wan
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WandaC-S
Hi， I am writing to seek your assistance with an issue I have encountered while using the iWhale pipeline. It is a highly efficient tool, and I appreciate its capability to manage reanalysis seamlessly from the point of failure. However, I have encountered an error, the details of which are as follows:
From my preliminary investigation, it appears that the issue might be related to GATK3 not recognizing the VCF file. I am not sure how to modify the command in docker pipeline. I would greatly appreciate it if you could provide some guidance on how to resolve this matter.
BR, Wan