alexcoppe / iwhale Goto Github PK

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 root@fcbac2e2eebc 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

Thank you for your pipeline first. I am confused about the output. For example, if "normal_sample" and "tumor_sample" are used as input. The merged vcf file will have four heads named tumor _sample, normal_sample, TUMOR, and NORMAL. Which one should I refer to if I want to know the mutations in the "tumor_sample". And what's the meaning of "TUMOR" and "NORMAL"? They have more mutations and don't seem to be duplicates of other columns.

Thank you for your work. It helps a lot.
Sometimes more than one tumor samples will refer to a same control. For example, we might have a pretreatment tumor sample (tumor_pre), a post treatment tumor sample (tumor_post), a post treatment lymph metastasis (tumor_ln_post) referring to a same blood control (control_sample). Now I put the working directory and the 'tumor_control_samples.txt' file in this way. It seems fine and works well:

$ ls
configuration.py  control_sample  tumor_control_samples.txt  tumor_ln_post  tumor_post  tumor_pre

$ cat tumor_control_samples.txt 
tumor_pre control_sample
tumor_post control_sample
tumor_ln_post control_sample

However, I am not sure whether this will cause any problems such as unnecessary recalculation or bias in the output file. For example, I know panel of normals (PONs) will be calculated by GATK, will one normal sample be used multiple times for calculation of PONs and cause problems?

Thanks for developing a pipeline which is supported by docker directly.
Sadly, I got an error while downloading the image.

failed to register layer: Error processing tar file(exit status 1): lchown /tmp/gatk3: invalid argument

Hi, thanks for your excellent job.
I want to download the WES data from Juvenile myelomonocytic leukemia patient in your paper, but I couldn't find the download link.
Could you tell me where the resource is ?