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sing-group / bicycle

bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis
http://www.sing-group.org/bicycle
GNU Lesser General Public License v3.0
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SEVERE: Error during execution - analyze-differential-methylation #10

Closed abedkurdi closed 3 years ago

abedkurdi commented 3 years ago

Hello guys, I am running bicycle analyze-differential-methylation to get differential methylation profiles for some regions of interests. Everything went OK until I run analyze-differential-methylation, I got the following exception:

SEVERE: Error during execution
java.lang.NullPointerException
    at es.cnio.bioinfo.bicycle.gatk.GPFilesReader.readLine(GPFilesReader.java:85)
    at es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis.analyzeDifferentialMethylationByBase(DifferentialMethylationAnalysis.java:360)
    at es.cnio.bioinfo.bicycle.cli.DifferentialMethylationAnalysisCommand.executeImpl(DifferentialMethylationAnalysisCommand.java:95)
    at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:52)
    at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86)
    at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

java.lang.NullPointerException
    at es.cnio.bioinfo.bicycle.gatk.GPFilesReader.readLine(GPFilesReader.java:85)
    at es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis.analyzeDifferentialMethylationByBase(DifferentialMethylationAnalysis.java:360)
    at es.cnio.bioinfo.bicycle.cli.DifferentialMethylationAnalysisCommand.executeImpl(DifferentialMethylationAnalysisCommand.java:95)
    at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:52)
    at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86)
    at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

Any idea what could be causing such an error?

Thank you in advance.

osvaldogc commented 3 years ago

Hi Abdullah,

Can you send the execution/command lines that you are using with bicycle? I mean all of them, from scratch, so we can try to follow your execution until you get the error.

Thanks.

Osvaldo Graña Castro, PhD Bioinformática Centro Nacional de Investigaciones Oncológicas, CNIO

@.*** Teléfono +34 91 732 8000 (ext. 3062)

Melchor Fernández Almagro, 3 28029 Madrid, España www.cnio.eshttps://www.cnio.es/

[CNIO stop cancer. Excelencia Severo Ochoa 2012-2019]http://www.cnio.es/ [https://apps.cnio.es/img/signature/hazte-amigo-es.jpg]

From: Abdullah El Kurdi @.*** Sent: Monday, April 26, 2021 1:58 PM To: sing-group/bicycle Cc: Subscribed Subject: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

Hello guys, I am running bicycle analyze-differential-methylation to get differential methylation profiles for some regions of interests. Everything went OK until I run analyze-differential-methylation, I got the following exception:

SEVERE: Error during execution java.lang.NullPointerException at es.cnio.bioinfo.bicycle.gatk.GPFilesReader.readLine(GPFilesReader.java:85) at es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis.analyzeDifferentialMethylationByBase(DifferentialMethylationAnalysis.java:360) at es.cnio.bioinfo.bicycle.cli.DifferentialMethylationAnalysisCommand.executeImpl(DifferentialMethylationAnalysisCommand.java:95) at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:52) at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86) at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

java.lang.NullPointerException at es.cnio.bioinfo.bicycle.gatk.GPFilesReader.readLine(GPFilesReader.java:85) at es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis.analyzeDifferentialMethylationByBase(DifferentialMethylationAnalysis.java:360) at es.cnio.bioinfo.bicycle.cli.DifferentialMethylationAnalysisCommand.executeImpl(DifferentialMethylationAnalysisCommand.java:95) at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:52) at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86) at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

Any idea what could be causing such an error?

Thank you in advance.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/sing-group/bicycle/issues/10, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADDOQK44KT6RCLO533B3DHTTKVIODANCNFSM43SXPSEA.

ADVERTENCIA LEGAL: Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protección de los datos personales de las personas físicas, la información personal que nos pueda facilitar a través de este correo electrónico quedará registrada por la Fundación CNIO con la finalidad de tramitar el objeto del presente correo electrónico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no serán comunicados a ningún destinatario salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. podrá ejercer los derechos de acceso, rectificación, supresión, limitación de tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el Delegado de Protección de Datos en: @.*** Para el caso de que Ud. precise conocer información adicional sobre el tratamiento de sus datos personales, puede consultar dicha información adicional en el siguiente enlace dentro de nuestra página web: https://www.cnio.es/es/privacidad/index.asp

LEGAL NOTICE: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message. Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protección de Datos) at: @.*** If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp

abedkurdi commented 3 years ago

Thank you for your quick response. First, I have made a new project using the following command:

java -jar ${bicycle} create-project \
    -p ~/project/1_ATAC_seq/methylation_analysis/analysis \
    -r ~/genome/m.musculus/mm10/fasta/ \
    -f ~/project/1_ATAC_seq/methylation_analysis/methylation_data \
    -b2 ~/software/bowtie2/ \
    -s ~/software/samtools-1.7_only_for_pneumocat \
    -m  _1.fastq

Then I made the reference bisulfation and indexing:

#Reference bisulfations
java -jar -Xmx200G ${bicycle} reference-bisulfitation \
    -p ~/project/1_ATAC_seq/methylation_analysis/analysis

#Reference-index - once for every assembly
java -jar -Xmx200G ${bicycle} reference-index \
    -p ~/project/1_ATAC_seq/methylation_analysis/analysis \
    -t 50

Then I mapped the reads to the newly made reference - from the previous step:

java -jar -Xmx200G ${bicycle} align \
    -p ~/project/1_ATAC_seq/methylation_analysis/analysis \
    -t 50 \
    -q2 phred33

Then I performed the methylation analysis:

java -jar -Xmx200G ${bicycle} analyze-methylation \
    -p ~/project/1_ATAC_seq/methylation_analysis/analysis \
    -t 50

Until here, everything worked well and no errors were thrown. Once I run differential methylation analysis:

java -jar -Xmx200G ${bicycle}  analyze-differential-methylation \
    -p ~/project/1_ATAC_seq/methylation_analysis/analysis \
    -c SRR11972155,SRR11972154,SRR11972152 \
    -t SRR11972151,SRR11972150,SRR11972149,SRR11972148,SRR11972147,SRR11972146,SRR11972145,SRR11972153 \
    -b ~/project/1_ATAC_seq/methylation_analysis/regions_of_interest/p90_atac_finalpeaks.bed

it starts like this:

Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase
INFO: Performing differential methylation at base level (DMC)
Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase
INFO: reference: /home/pk3/genome/m.musculus/mm10/fasta/mm10.fa
Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase
INFO: treament samples: [SRR11972151, SRR11972150, SRR11972149, SRR11972148, SRR11972147, SRR11972146, SRR11972145, SRR11972153]
Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase
INFO: control samples: [SRR11972155, SRR11972154, SRR11972152]
Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase
INFO: Computing DMCs...

and then, a few minutes later, the error is thrown:

SEVERE: Error during execution
java.lang.NullPointerException
    at es.cnio.bioinfo.bicycle.gatk.GPFilesReader.readLine(GPFilesReader.java:85)
    at es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis.analyzeDifferentialMethylationByBase(DifferentialMethylationAnalysis.java:360)
    at es.cnio.bioinfo.bicycle.cli.DifferentialMethylationAnalysisCommand.executeImpl(DifferentialMethylationAnalysisCommand.java:95)
    at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:52)
    at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86)
    at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

java.lang.NullPointerException
    at es.cnio.bioinfo.bicycle.gatk.GPFilesReader.readLine(GPFilesReader.java:85)
    at es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis.analyzeDifferentialMethylationByBase(DifferentialMethylationAnalysis.java:360)
    at es.cnio.bioinfo.bicycle.cli.DifferentialMethylationAnalysisCommand.executeImpl(DifferentialMethylationAnalysisCommand.java:95)
    at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:52)
    at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86)
    at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

I appreciate your help, Thank you very much.

osvaldogc commented 3 years ago

Dear Abdullah,

Could you please share with us the following files from your bicycle output?

(1) All "*.methylcytosines" files within the "workingDirectory".

(2) A file called "mm10.index" within the reference directory.

So we could try to find out what the problem is with your execution.

Thanks.

osvaldo

Osvaldo Graña Castro, PhD Bioinformática Centro Nacional de Investigaciones Oncológicas, CNIO

@.*** Teléfono +34 91 732 8000 (ext. 3062)

Melchor Fernández Almagro, 3 28029 Madrid, España www.cnio.eshttps://www.cnio.es/

[CNIO stop cancer. Excelencia Severo Ochoa 2012-2019]http://www.cnio.es/ [https://apps.cnio.es/img/signature/hazte-amigo-es.jpg]

From: Abdullah El Kurdi @.*** Sent: Wednesday, April 28, 2021 7:33 AM To: sing-group/bicycle Cc: Graña.Osvaldo; Comment Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

Thank you for your quick response. First, I have made a new project using the following command:

java -jar ${bicycle} create-project \ -p ~/project/1_ATAC_seq/methylation_analysis/analysis \ -r ~/genome/m.musculus/mm10/fasta/ \ -f ~/project/1_ATAC_seq/methylation_analysis/methylation_data \ -b2 ~/software/bowtie2/ \ -s ~/software/samtools-1.7_only_for_pneumocat \ -m _1.fastq

Then I made the reference bisulfation and indexing:

Reference bisulfations

java -jar -Xmx200G ${bicycle} reference-bisulfitation \ -p ~/project/1_ATAC_seq/methylation_analysis/analysis

Reference-index - once for every assembly

java -jar -Xmx200G ${bicycle} reference-index \ -p ~/project/1_ATAC_seq/methylation_analysis/analysis \ -t 50

Then I mapped the reads to the newly made reference - from the previous step:

java -jar -Xmx200G ${bicycle} align \ -p ~/project/1_ATAC_seq/methylation_analysis/analysis \ -t 50 \ -q2 phred33

Then I performed the methylation analysis:

java -jar -Xmx200G ${bicycle} analyze-methylation \ -p ~/project/1_ATAC_seq/methylation_analysis/analysis \ -t 50

Until here, everything worked well and no errors were thrown. Once I run differential methylation analysis:

java -jar -Xmx200G ${bicycle} analyze-differential-methylation \ -p ~/project/1_ATAC_seq/methylation_analysis/analysis \ -c SRR11972155,SRR11972154,SRR11972152 \ -t SRR11972151,SRR11972150,SRR11972149,SRR11972148,SRR11972147,SRR11972146,SRR11972145,SRR11972153 \ -b ~/project/1_ATAC_seq/methylation_analysis/regions_of_interest/p90_atac_finalpeaks.bed

it starts like this:

Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase INFO: Performing differential methylation at base level (DMC) Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase INFO: reference: /home/pk3/genome/m.musculus/mm10/fasta/mm10.fa Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase INFO: treament samples: [SRR11972151, SRR11972150, SRR11972149, SRR11972148, SRR11972147, SRR11972146, SRR11972145, SRR11972153] Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase INFO: control samples: [SRR11972155, SRR11972154, SRR11972152] Apr 28, 2021 8:28:18 AM es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis analyzeDifferentialMethylationByBase INFO: Computing DMCs...

and then, a few minutes later, the error is thrown:

SEVERE: Error during execution java.lang.NullPointerException at es.cnio.bioinfo.bicycle.gatk.GPFilesReader.readLine(GPFilesReader.java:85) at es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis.analyzeDifferentialMethylationByBase(DifferentialMethylationAnalysis.java:360) at es.cnio.bioinfo.bicycle.cli.DifferentialMethylationAnalysisCommand.executeImpl(DifferentialMethylationAnalysisCommand.java:95) at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:52) at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86) at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

java.lang.NullPointerException at es.cnio.bioinfo.bicycle.gatk.GPFilesReader.readLine(GPFilesReader.java:85) at es.cnio.bioinfo.bicycle.operations.DifferentialMethylationAnalysis.analyzeDifferentialMethylationByBase(DifferentialMethylationAnalysis.java:360) at es.cnio.bioinfo.bicycle.cli.DifferentialMethylationAnalysisCommand.executeImpl(DifferentialMethylationAnalysisCommand.java:95) at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:52) at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86) at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

I appreciate your help, Thank you very much.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/sing-group/bicycle/issues/10#issuecomment-828156887, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADDOQK7I3WS3T4QXN34FDCTTK6M4PANCNFSM43SXPSEA.

ADVERTENCIA LEGAL: Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protección de los datos personales de las personas físicas, la información personal que nos pueda facilitar a través de este correo electrónico quedará registrada por la Fundación CNIO con la finalidad de tramitar el objeto del presente correo electrónico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no serán comunicados a ningún destinatario salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. podrá ejercer los derechos de acceso, rectificación, supresión, limitación de tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el Delegado de Protección de Datos en: @.*** Para el caso de que Ud. precise conocer información adicional sobre el tratamiento de sus datos personales, puede consultar dicha información adicional en el siguiente enlace dentro de nuestra página web: https://www.cnio.es/es/privacidad/index.asp

LEGAL NOTICE: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message. Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protección de Datos) at: @.*** If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp

abedkurdi commented 3 years ago

How would you like me to send you those files? Any email you can share with me? Thanks in advance.

osvaldogc commented 3 years ago

@.***

Place all the files in a common folder and later compress it, please.

Thanks

Osvaldo Graña Castro, PhD Bioinformática Centro Nacional de Investigaciones Oncológicas, CNIO

@.*** Teléfono +34 91 732 8000 (ext. 3062)

Melchor Fernández Almagro, 3 28029 Madrid, España www.cnio.eshttps://www.cnio.es/

[CNIO stop cancer. Excelencia Severo Ochoa 2012-2019]http://www.cnio.es/ [https://apps.cnio.es/img/signature/hazte-amigo-es.jpg]

From: Abdullah El Kurdi @.*** Sent: Wednesday, April 28, 2021 10:26 AM To: sing-group/bicycle Cc: Graña.Osvaldo; Comment Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

How would you like me to send you those files? Any email we can share with me? Thanks in advance.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/sing-group/bicycle/issues/10#issuecomment-828258301, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADDOQK2F6D2WL2KVWXLOD7TTK7BCJANCNFSM43SXPSEA.

ADVERTENCIA LEGAL: Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protección de los datos personales de las personas físicas, la información personal que nos pueda facilitar a través de este correo electrónico quedará registrada por la Fundación CNIO con la finalidad de tramitar el objeto del presente correo electrónico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no serán comunicados a ningún destinatario salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. podrá ejercer los derechos de acceso, rectificación, supresión, limitación de tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el Delegado de Protección de Datos en: @.*** Para el caso de que Ud. precise conocer información adicional sobre el tratamiento de sus datos personales, puede consultar dicha información adicional en el siguiente enlace dentro de nuestra página web: https://www.cnio.es/es/privacidad/index.asp

LEGAL NOTICE: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message. Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protección de Datos) at: @.*** If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp

abedkurdi commented 3 years ago

Sorry I cannot see your e-mail, I see stars only would you like to reply by email?

abedkurdi commented 3 years ago

Abdullah El Kurdi has shared a OneDrive file with you. To view it, click the link below. https://1drv.ms/u/s!AjPDO0Q2jP2piwBsercSQvy6ev_i [https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]https://1drv.ms/u/s!AjPDO0Q2jP2piwBsercSQvy6ev_i methylcytosines_and_index_files.ziphttps://1drv.ms/u/s!AjPDO0Q2jP2piwBsercSQvy6ev_i

Kindly check the attached ZIP file, which contains all methylcytosines files and the genome index.

Thank you.

From: osvaldogc @.> Sent: Wednesday, April 28, 2021 11:40 AM To: sing-group/bicycle @.> Cc: Abdullah El Kurdi @.>; Author @.> Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

@.***

Place all the files in a common folder and later compress it, please.

Thanks

Osvaldo Graña Castro, PhD Bioinformática Centro Nacional de Investigaciones Oncológicas, CNIO

@.*** Teléfono +34 91 732 8000 (ext. 3062)

Melchor Fernández Almagro, 3 28029 Madrid, España www.cnio.eshttps://www.cnio.es/

[CNIO stop cancer. Excelencia Severo Ochoa 2012-2019]http://www.cnio.es/ [https://apps.cnio.es/img/signature/hazte-amigo-es.jpg]

From: Abdullah El Kurdi @.*** Sent: Wednesday, April 28, 2021 10:26 AM To: sing-group/bicycle Cc: Graña.Osvaldo; Comment Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

How would you like me to send you those files? Any email we can share with me? Thanks in advance.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/sing-group/bicycle/issues/10#issuecomment-828258301, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADDOQK2F6D2WL2KVWXLOD7TTK7BCJANCNFSM43SXPSEA.

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osvaldogc commented 3 years ago

Thank you Abdullah.

Let us go through it, please.

osvaldo

From: Abdullah El Kurdi @.*** Sent: Wednesday, April 28, 2021 10:59 AM To: sing-group/bicycle Cc: Graña.Osvaldo; Comment Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

Abdullah El Kurdi has shared a OneDrive file with you. To view it, click the link below. https://1drv.ms/u/s!AjPDO0Q2jP2piwBsercSQvy6ev_i [https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]https://1drv.ms/u/s!AjPDO0Q2jP2piwBsercSQvy6ev_i methylcytosines_and_index_files.ziphttps://1drv.ms/u/s!AjPDO0Q2jP2piwBsercSQvy6ev_i

Kindly check the attached ZIP file, which contains all methylcytosines files and the genome index.

Thank you.

From: osvaldogc @.> Sent: Wednesday, April 28, 2021 11:40 AM To: sing-group/bicycle @.> Cc: Abdullah El Kurdi @.>; Author @.> Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

@.***

Place all the files in a common folder and later compress it, please.

Thanks

Osvaldo Graña Castro, PhD Bioinformática Centro Nacional de Investigaciones Oncológicas, CNIO

@.*** Teléfono +34 91 732 8000 (ext. 3062)

Melchor Fernández Almagro, 3 28029 Madrid, España www.cnio.eshttps://www.cnio.es/

[CNIO stop cancer. Excelencia Severo Ochoa 2012-2019]http://www.cnio.es/ [https://apps.cnio.es/img/signature/hazte-amigo-es.jpg]

From: Abdullah El Kurdi @.*** Sent: Wednesday, April 28, 2021 10:26 AM To: sing-group/bicycle Cc: Graña.Osvaldo; Comment Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe

How would you like me to send you those files? Any email we can share with me? Thanks in advance.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/sing-group/bicycle/issues/10#issuecomment-828258301, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADDOQK2F6D2WL2KVWXLOD7TTK7BCJANCNFSM43SXPSEA.

ADVERTENCIA LEGAL: Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protección de los datos personales de las personas físicas, la información personal que nos pueda facilitar a través de este correo electrónico quedará registrada por la Fundación CNIO con la finalidad de tramitar el objeto del presente correo electrónico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no serán comunicados a ningún destinatario salvo a aquellos que usted nos autorice o así venga exigido por una ley. Ud. podrá ejercer los derechos de acceso, rectificación, supresión, limitación de tratamiento, portabilidad y oposición en la siguiente dirección: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podrá ponerse en contacto con el Delegado de Protección de Datos en: @.*** Para el caso de que Ud. precise conocer información adicional sobre el tratamiento de sus datos personales, puede consultar dicha información adicional en el siguiente enlace dentro de nuestra página web: https://www.cnio.es/es/privacidad/index.asp

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lipido commented 3 years ago

Dear Abdullah,

Could you please check if there is a file called "mm10.fa.index" in the workingDirectory of the project (please note the ".index" extension, instead of ".fai")? If so, please send it to us.

Cheers,

Daniel.

abedkurdi commented 3 years ago

Thank you very much for your effort.

Yes indeed, I have "mm10.fa.index" file. please find it attached.

Thanks a lot. Abed

From: Daniel Glez-Peña @.> Sent: Tuesday, May 4, 2021 10:59 AM To: sing-group/bicycle @.> Cc: Abdullah El Kurdi @.>; Author @.> Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

Dear Abdullah,

Could you please check if there is a file called "mm10.fa.index" in the workingDirectory of the project (please note the ".index" extension, instead of ".fai")?

Cheers,

Daniel.

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lipido commented 3 years ago

Where it is attached? I can't find it in your email. If you have attached it, please compress it as .zip (maybe a spam filter in the middle removed it)

abedkurdi commented 3 years ago

Here we go.

Thanks again.

From: Daniel Glez-Peña @.> Sent: Tuesday, May 4, 2021 11:37 AM To: sing-group/bicycle @.> Cc: Abdullah El Kurdi @.>; Author @.> Subject: Re: [sing-group/bicycle] SEVERE: Error during execution - analyze-differential-methylation (#10)

Where it is attached? I can't find it in your email. If you have attached it, please compress it as .zip (maybe a spam filter in the middle removed it)

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lipido commented 3 years ago

Mmmmm, nope. Send a direct email to me attaching the file: dgpena@uvigo.es

abedkurdi commented 3 years ago

I fixed the problem. It was in the index file, not properly made because my computer has frozen at some point, and the index file contained only chromosomes 1 to 6. When I included all the chromosomes, everything went perfectly.

Thanks for your support!