CLASSPATH of GATK version 4.4.0.0

Question

CLASSPATH of GATK version 4.4.0.0

jinyanjane opened this issue 2 years ago · 4 comments

I met a problem with run CFSAN SNP pipeline. Error: CLASSPATH is not configured with the path to GenomeAnalysisTK.jar.
I have installed the lastest GATK version 4.4.0.0. And in my ~/.bashrc file, the classfath setting is: export CLASSPATH=/root/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar:$CLASSPATH

I have checked the path and everything is fine in my sense. Can you help me? It is an urgency.

Thank you.

Answer 1 · 2023-05-04T07:14:59.000Z

CFSAN SNP Pipeline isn't compatible with GATK 4, unfortunately. You'll have to obtain the jar for GATK 3.8 and add that to your classpath. Justin

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On Wed, May 3, 2023 at 7:29 PM jinyanjane ***@***.***> wrote: I met a problem with run CFSAN SNP pipeline. Error: CLASSPATH is not configured with the path to GenomeAnalysisTK.jar. I have installed the lastest GATK version 4.4.0.0. And in my ~/.bashrc file, the classfath setting is: export CLASSPATH=/root/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar:$CLASSPATH I have checked the path and everything is fine in my sense. Can you help me? It is an urgency. Thank you. — Reply to this email directly, view it on GitHub <#26>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIFUSUZFTMEFIJUCRDWRYTXEJFSZANCNFSM6AAAAAAXUKYVEM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

Answer 2 · 2023-05-04T07:19:30.000Z

Hi Justin， Thank you for your help. I have not found the GATK 3.8 of the jar file on the Internet, are you willing to share the download link to me. Much appreciated. Jane 获取 Outlook for iOS<https://aka.ms/o0ukef>

________________________________ 发件人: Justin Payne ***@***.***> 发送时间: Thursday, May 4, 2023 3:15:10 PM 收件人: CFSAN-Biostatistics/snp-pipeline ***@***.***> 抄送: Jane Jin ***@***.***>; Author ***@***.***> 主题: Re: [CFSAN-Biostatistics/snp-pipeline] CLASSPATH of GATK version 4.4.0.0 (Issue #26) CAUTION: EXTERNAL EMAIL - Sent from an email domain that is not formally trusted by Eurofins. Do not click on links or open attachments unless you recognise the sender and are certain that the content is safe. CFSAN SNP Pipeline isn't compatible with GATK 4, unfortunately. You'll have to obtain the jar for GATK 3.8 and add that to your classpath. Justin

On Wed, May 3, 2023 at 7:29 PM jinyanjane ***@***.***> wrote: I met a problem with run CFSAN SNP pipeline. Error: CLASSPATH is not configured with the path to GenomeAnalysisTK.jar. I have installed the lastest GATK version 4.4.0.0. And in my ~/.bashrc file, the classfath setting is: export CLASSPATH=/root/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar:$CLASSPATH I have checked the path and everything is fine in my sense. Can you help me? It is an urgency. Thank you. — Reply to this email directly, view it on GitHub <#26>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIFUSUZFTMEFIJUCRDWRYTXEJFSZANCNFSM6AAAAAAXUKYVEM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub<#26 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A2CEQXZZMV2QZYC2SNEAVG3XENJP5ANCNFSM6AAAAAAXUKYVEM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

Answer 3 · 2023-05-04T08:06:59.000Z

You should be able to grab it from here: https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2 Let me know if that doesn't work.

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On Thu, May 4, 2023 at 2:19 PM jinyanjane ***@***.***> wrote: Hi Justin， Thank you for your help. I have not found the GATK 3.8 of the jar file on the Internet, are you willing to share the download link to me. Much appreciated. Jane 获取 Outlook for iOS<https://aka.ms/o0ukef> ________________________________ 发件人: Justin Payne ***@***.***> 发送时间: Thursday, May 4, 2023 3:15:10 PM 收件人: CFSAN-Biostatistics/snp-pipeline ***@***.***> 抄送: Jane Jin ***@***.***>; Author ***@***.***> 主题: Re: [CFSAN-Biostatistics/snp-pipeline] CLASSPATH of GATK version 4.4.0.0 (Issue #26) CAUTION: EXTERNAL EMAIL - Sent from an email domain that is not formally trusted by Eurofins. Do not click on links or open attachments unless you recognise the sender and are certain that the content is safe. CFSAN SNP Pipeline isn't compatible with GATK 4, unfortunately. You'll have to obtain the jar for GATK 3.8 and add that to your classpath. Justin On Wed, May 3, 2023 at 7:29 PM jinyanjane ***@***.***> wrote: > I met a problem with run CFSAN SNP pipeline. Error: CLASSPATH is not > configured with the path to GenomeAnalysisTK.jar. > I have installed the lastest GATK version 4.4.0.0. And in my ~/.bashrc > file, the classfath setting is: export > CLASSPATH=/root/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar:$CLASSPATH > > I have checked the path and everything is fine in my sense. Can you help > me? It is an urgency. > > Thank you. > > — > Reply to this email directly, view it on GitHub > <#26>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAIFUSUZFTMEFIJUCRDWRYTXEJFSZANCNFSM6AAAAAAXUKYVEM> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > — Reply to this email directly, view it on GitHub< #26 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/A2CEQXZZMV2QZYC2SNEAVG3XENJP5ANCNFSM6AAAAAAXUKYVEM>. You are receiving this because you authored the thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub <#26 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIFUSXOKBLO3234WOD4I5LXENKA3ANCNFSM6AAAAAAXUKYVEM> . You are receiving this because you commented.Message ID: ***@***.***>

Answer 4 · 2023-05-04T10:44:35.000Z

You should be able to grab it from here: https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2 Let me know if that doesn't work.
…
On Thu, May 4, 2023 at 2:19 PM jinyanjane @.> wrote: Hi Justin， Thank you for your help. I have not found the GATK 3.8 of the jar file on the Internet, are you willing to share the download link to me. Much appreciated. Jane 获取 Outlook for iOShttps://aka.ms/o0ukef ________________________________ 发件人: Justin Payne @.> 发送时间: Thursday, May 4, 2023 3:15:10 PM 收件人: CFSAN-Biostatistics/snp-pipeline @.> 抄送: Jane Jin @.>; Author @.> 主题: Re: [CFSAN-Biostatistics/snp-pipeline] CLASSPATH of GATK version 4.4.0.0 (Issue #26) CAUTION: EXTERNAL EMAIL - Sent from an email domain that is not formally trusted by Eurofins. Do not click on links or open attachments unless you recognise the sender and are certain that the content is safe. CFSAN SNP Pipeline isn't compatible with GATK 4, unfortunately. You'll have to obtain the jar for GATK 3.8 and add that to your classpath. Justin On Wed, May 3, 2023 at 7:29 PM jinyanjane @.> wrote: > I met a problem with run CFSAN SNP pipeline. Error: CLASSPATH is not > configured with the path to GenomeAnalysisTK.jar. > I have installed the lastest GATK version 4.4.0.0. And in my ~/.bashrc > file, the classfath setting is: export > CLASSPATH=/root/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar:$CLASSPATH > > I have checked the path and everything is fine in my sense. Can you help > me? It is an urgency. > > Thank you. > > — > Reply to this email directly, view it on GitHub > <#26>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAIFUSUZFTMEFIJUCRDWRYTXEJFSZANCNFSM6AAAAAAXUKYVEM> > . > You are receiving this because you are subscribed to this thread.Message > ID: @.> > — Reply to this email directly, view it on GitHub< #26 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/A2CEQXZZMV2QZYC2SNEAVG3XENJP5ANCNFSM6AAAAAAXUKYVEM>. You are receiving this because you authored the thread.Message ID: @.> — Reply to this email directly, view it on GitHub <#26 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIFUSXOKBLO3234WOD4I5LXENKA3ANCNFSM6AAAAAAXUKYVEM . You are receiving this because you commented.Message ID: @.***>

Hi Justin,
I download “GenomeAnalysisTK.jar” from the link that you provided. When I put the jar file into my linux work directory and set Environment Variables of PATH and CLASSPATH for GATK. Next, I ran the CFSAN SNP pipeline, got ERROR as blow.

(base) root@DESKTOP-K6PUB49:~# cfsan_snp_pipeline run -o snppipeline/Salmonella/output -s snppipeline/Salmonella/sample snppipeline/Salmonella/reference/NCTC7832.fasta
Checking dependencies...
##### 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: Malformed walker argument: Could not find walker with name: IndelRealigner
##### ERROR ------------------------------------------------------------------------------------------

Check the SNP Pipeline installation instructions here: http://snp-pipeline.readthedocs.org/en/latest/installation.html