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jyhehir / mobster

For more details about Mobster please see
https://jyhehir.github.io/mobster/index.html
GNU General Public License v3.0
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Problem using Mobster #32

Closed meboussaha closed 4 years ago

meboussaha commented 4 years ago

Dear Sir, I have been using Mobster (MobileInsertions-1.0-SNAPSHOT.jar) to study TEs in cattle WGS. Today and with the availability of a new cattle reference genome we have realigned all our data against this new reference genome using the bwa-mem aligner. Unfortunately we are getting an error when executing the same pipeline (with MobileInsertions-1.0-SNAPSHOT.jar). Here is a screen shot of the rror. Any help? Thaks in advance Mekki mobster_error

jyhehir commented 4 years ago

Hi, Can you please confirm if the data is paired-end?And if you are able to download an built it yourself? Regards,Jayne On Tuesday, 29 October 2019, 02:39:45 pm GMT+1, meboussaha notifications@github.com wrote:

Dear Sir, I have been using Mobster (MobileInsertions-1.0-SNAPSHOT.jar) to study TEs in cattle WGS. Today and with the availability of a new cattle reference genome we have realigned all our data against this new reference genome using the bwa-mem aligner. Unfortunately we are getting an error when executing the same pipeline (with MobileInsertions-1.0-SNAPSHOT.jar). Here is a screen shot of the rror. Any help? Thaks in advance Mekki

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meboussaha commented 4 years ago

Dear Sir, Yes the data is paired-end and its our bioinformatics facility that succesfully downloaded the mobster-0.2.4.1 version. I copied the «MobileInsertions-1.0-SNAPSHOT.jar » in the target directory. Regards Mekki

De : jyhehir notifications@github.com Envoyé : jeudi 31 octobre 2019 16:19 À : jyhehir/mobster mobster@noreply.github.com Cc : Mekki Boussaha mekki.boussaha@inra.fr; Author author@noreply.github.com Objet : Re: [jyhehir/mobster] Problem using Mobster (#32)

Hi, Can you please confirm if the data is paired-end?And if you are able to download an built it yourself? Regards,Jayne On Tuesday, 29 October 2019, 02:39:45 pm GMT+1, meboussaha notifications@github.com<mailto:notifications@github.com> wrote:

Dear Sir, I have been using Mobster (MobileInsertions-1.0-SNAPSHOT.jar) to study TEs in cattle WGS. Today and with the availability of a new cattle reference genome we have realigned all our data against this new reference genome using the bwa-mem aligner. Unfortunately we are getting an error when executing the same pipeline (with MobileInsertions-1.0-SNAPSHOT.jar). Here is a screen shot of the rror. Any help? Thaks in advance Mekki

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jyhehir commented 4 years ago

Dear Mekki, I have just cloned the repository to double check. After cloning, and running the install.sh I would expect that you generate a jar file in the target directory which is called MobileInsertions-0.2.4.1.jar This version of Mobster has support for bwa_mem, which I assume you are using as aligner?Alternatively you can try running picard tools standalone on your bam to confirm that the insert size can be computed. Regards,Jayne On Thursday, 31 October 2019, 05:48:03 pm GMT+1, meboussaha notifications@github.com wrote:

Dear Sir, Yes the data is paired-end and its our bioinformatics facility that succesfully downloaded the mobster-0.2.4.1 version. I copied the «MobileInsertions-1.0-SNAPSHOT.jar » in the target directory. Regards Mekki

De : jyhehir notifications@github.com Envoyé : jeudi 31 octobre 2019 16:19 À : jyhehir/mobster mobster@noreply.github.com Cc : Mekki Boussaha mekki.boussaha@inra.fr; Author author@noreply.github.com Objet : Re: [jyhehir/mobster] Problem using Mobster (#32)

Hi, Can you please confirm if the data is paired-end?And if you are able to download an built it yourself? Regards,Jayne On Tuesday, 29 October 2019, 02:39:45 pm GMT+1, meboussaha notifications@github.com<mailto:notifications@github.com> wrote:

Dear Sir, I have been using Mobster (MobileInsertions-1.0-SNAPSHOT.jar) to study TEs in cattle WGS. Today and with the availability of a new cattle reference genome we have realigned all our data against this new reference genome using the bwa-mem aligner. Unfortunately we are getting an error when executing the same pipeline (with MobileInsertions-1.0-SNAPSHOT.jar). Here is a screen shot of the rror. Any help? Thaks in advance Mekki

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meboussaha commented 4 years ago

Hi, Thanks a ot for your help. I solved the problem recently by using the MobileInsertions-0.2.4.1.jar and the option bwa-mem. Regards Mekki

De : jyhehir notifications@github.com Envoyé : mardi 5 novembre 2019 16:18 À : jyhehir/mobster mobster@noreply.github.com Cc : Mekki Boussaha mekki.boussaha@inra.fr; Author author@noreply.github.com Objet : Re: [jyhehir/mobster] Problem using Mobster (#32)

Dear Mekki, I have just cloned the repository to double check. After cloning, and running the install.sh I would expect that you generate a jar file in the target directory which is called MobileInsertions-0.2.4.1.jar This version of Mobster has support for bwa_mem, which I assume you are using as aligner?Alternatively you can try running picard tools standalone on your bam to confirm that the insert size can be computed. Regards,Jayne On Thursday, 31 October 2019, 05:48:03 pm GMT+1, meboussaha notifications@github.com<mailto:notifications@github.com> wrote:

Dear Sir, Yes the data is paired-end and its our bioinformatics facility that succesfully downloaded the mobster-0.2.4.1 version. I copied the «MobileInsertions-1.0-SNAPSHOT.jar » in the target directory. Regards Mekki

De : jyhehir notifications@github.com<mailto:notifications@github.com> Envoyé : jeudi 31 octobre 2019 16:19 À : jyhehir/mobster mobster@noreply.github.com<mailto:mobster@noreply.github.com> Cc : Mekki Boussaha mekki.boussaha@inra.fr<mailto:mekki.boussaha@inra.fr>; Author author@noreply.github.com<mailto:author@noreply.github.com> Objet : Re: [jyhehir/mobster] Problem using Mobster (#32)

Hi, Can you please confirm if the data is paired-end?And if you are able to download an built it yourself? Regards,Jayne On Tuesday, 29 October 2019, 02:39:45 pm GMT+1, meboussaha notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> wrote:

Dear Sir, I have been using Mobster (MobileInsertions-1.0-SNAPSHOT.jar) to study TEs in cattle WGS. Today and with the availability of a new cattle reference genome we have realigned all our data against this new reference genome using the bwa-mem aligner. Unfortunately we are getting an error when executing the same pipeline (with MobileInsertions-1.0-SNAPSHOT.jar). Here is a screen shot of the rror. Any help? Thaks in advance Mekki

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