How to add an explicit type tag :NAME in gatk3/GenomeAnalysisTK.jar? #3
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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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Hi @alexcoppe, I will keep you updated on the progress and results. Best |
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Ok, thank you, keep me updated!
Alessandro
…On Tue, Jul 23, 2024 at 3:37 AM WandaWanda ***@***.***> wrote:
Hi Alessandro,
Thank you for your response. I have encountered a hiccup with the pipeline
due to my initial unfamiliarity with the database folder hierarchy and the
VEP database. I will now rerun the pipeline from the beginning.
I will keep you updated on the progress and results.
Best
Wan
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Hi @alexcoppe, |
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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
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