terminate called after throwing an instance of 'boost::exception_detail::clone_impl<portcullis::JunctionException>' what(): std::exception**

[fcamara7]

Hello,

We have been trying to install portcullis (1.0.2) in our cluster for a few days as I would like to test in the context of mikado. Unfortunately we have not been able to do so thus far. We have only been able to get the "portcullis prep" part of the program to work.

"portcullis junc" crashes with the following (cryptic?) message:

terminate called after throwing an instance of 'boost::exception_detail::clone_impl' what(): std::exception

command line: portcullis junc -t 5 -v /users/rg/fcamara/projects/hiSeqvsPacBio/portcullishg38.chroms.fa

Have you seen this type of error before??

We installed the program in a cluster using the modules for Python 3.6.1, GCC-6.3.0 and Boost 1.63.0.

(./configure --prefix=/software/as/el7.2/portcullis-1.0.2 --with-boost-libdir=/software/as/el7.2/EasyBuild/CRG/software/Boost/1.63.0-foss-2017a/lib --with-zlib=/software/as/el7.2/EasyBuild/CRG/software/zlib/1.2.11-GCCcore-6.3.0/lib)

I should perhaps point out that the BAM file contains sequences (non-chromosomal) that are not included in the human genome assembly I want to analyze, which only contains the 24 chromosomes..I don't think the issue lies here but perhaps...

One final (unrelated issue). After finally being able to install portcullis we are still not able to get the binary "junctools" to work. It gives us the following error:

./junctools /software/as/el7.2/EasyBuild/CRG/software/Python/3.6.1-foss-2017a/bin/python3: error while loading shared libraries: libpython3.6m.so.1.0: cannot open shared object file

Thanks for your help and do let me know if you need more info...

err2.gz

[maplesond]

Sorry to here you are having trouble with portcullis. I'll try to address each issue.

With regards to installation I'll make a singularity container shortly which will address both the portcullis and junctools installation issues.

The junctools installation issue sounds like it isnt correctly hooked into your python installation. If you want to install it directly you could type "python3 setup.py install" in the junctools directory although the build system should allow it to build ok. Then to run you just need the pythonpath configured correctly.

For portcullis junc I'll try to improve the error reporting in future releases however there are 2 problens here. The first is that as you identified the bam must contain the same target sequences as the reference. The second is that it looks like the command line is incomplete. Normally for this stage you would have to point it at the output directory of the prep stage.

Sorry if the instructions above are a bit vague as I'm away from a computer for now. Let me know if you need further help and I'll get back to you as soon as possible.

Sent from my Samsung Galaxy smartphone.

-------- Original message -------- From: fcamara7 notifications@github.com Date: 06/10/2017 16:41 (GMT+00:00) To: maplesond/portcullis portcullis@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [maplesond/portcullis] terminate called after throwing an instance ofhelp needed: 'boost::exception_detail::clone_impl' what(): std::exception** (#25)

Hello,

We have been trying to install portcullis (1.0.2) in our cluster for a few days as I would like to test in the context of mikado. Unfortunately we have not been able to do so thus far. We have only been able to get the "portcullis prep" part of the program to work.

"portcullis junc" crashes with the following (cryptic?) message:

terminate called after throwing an instance of 'boost::exception_detail::clone_implportcullis::JunctionException' what(): std::exception

command line: portcullis junc -t 5 -v /users/rg/fcamara/projects/hiSeqvsPacBio/portcullishg38.chroms.fa

Have you seen this type of error before??

We installed the program in the cluster using with Python 3.6.1 and Boost 1.63.0.

I should perhaps point out that the BAM file contains sequences (non-chromosomal) that are not included in the human genome assembly I want to analyze, which only contains the 24 chromosomes..I don't think the issue lies here but perhaps...

One final (unrelated issue). After finally being able to install portcullis we are still not able to get the binary "junctools" to work. It gives us the following error:

./junctools /software/as/el7.2/EasyBuild/CRG/software/Python/3.6.1-foss-2017a/bin/python3: error while loading shared libraries: libpython3.6m.so.1.0: cannot open shared object file

Thanks for your help and do let me know if you need more info...

err2.gzhttps://github.com/maplesond/portcullis/files/1363179/err2.gz

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[fcamara7]

Hi Daniel,

Thanks for the very quick reply! I will try to implement your suggestions, most likely on Monday.

btw "/users/rg/fcamara/projects/hiSeqvsPacBio/portcullishg38.chroms.fa/" is actually a directory (containing the output of prep).

Cheers and have a nice weekend.

Francisco

On Fri, Oct 6, 2017 at 6:36 PM, Daniel Mapleson notifications@github.com wrote:

Sorry to here you are having trouble with portcullis. I'll try to address each issue.

With regards to installation I'll make a singularity container shortly which will address both the portcullis and junctools installation issues.

The junctools installation issue sounds like it isnt correctly hooked into your python installation. If you want to install it directly you could type "python3 setup.py install" in the junctools directory although the build system should allow it to build ok. Then to run you just need the pythonpath configured correctly.

For portcullis junc I'll try to improve the error reporting in future releases however there are 2 problens here. The first is that as you identified the bam must contain the same target sequences as the reference. The second is that it looks like the command line is incomplete. Normally for this stage you would have to point it at the output directory of the prep stage.

Sorry if the instructions above are a bit vague as I'm away from a computer for now. Let me know if you need further help and I'll get back to you as soon as possible.

Sent from my Samsung Galaxy smartphone.

-------- Original message -------- From: fcamara7 notifications@github.com Date: 06/10/2017 16:41 (GMT+00:00) To: maplesond/portcullis portcullis@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [maplesond/portcullis] terminate called after throwing an instance ofhelp needed: 'boost::exception_detail::clone_impl' what(): std::exception** (#25)

Hello,

We have been trying to install portcullis (1.0.2) in our cluster for a few days as I would like to test in the context of mikado. Unfortunately we have not been able to do so thus far. We have only been able to get the "portcullis prep" part of the program to work.

"portcullis junc" crashes with the following (cryptic?) message:

terminate called after throwing an instance of 'boost::exception_detail:: clone_implportcullis::JunctionException' what(): std::exception

command line: portcullis junc -t 5 -v /users/rg/fcamara/projects/ hiSeqvsPacBio/portcullishg38.chroms.fa

Have you seen this type of error before??

We installed the program in the cluster using with Python 3.6.1 and Boost 1.63.0.

I should perhaps point out that the BAM file contains sequences (non-chromosomal) that are not included in the human genome assembly I want to analyze, which only contains the 24 chromosomes..I don't think the issue lies here but perhaps...

One final (unrelated issue). After finally being able to install portcullis we are still not able to get the binary "junctools" to work. It gives us the following error:

./junctools /software/as/el7.2/EasyBuild/CRG/software/Python/3.6.1-foss-2017a/bin/python3: error while loading shared libraries: libpython3.6m.so.1.0: cannot open shared object file

Thanks for your help and do let me know if you need more info...

err2.gzhttps://github.com/maplesond/portcullis/files/1363179/err2.gz

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[maplesond]

Hi Francisco,

Ah ok. So then it's likely that the discrepancy between the reference fasta and the BAM will likely explain your issue. You could use samtools to strip the BAM of any alignments to target sequences not in the reference.

I have just added a singularity image here: https://github.com/maplesond/portcullis/releases/download/Release-1.0.2/portcullis-1.0.2-singularity.img It contains two apps: portcullis and junctools. I'm keen to get some feedback on this as it's the first time I've built a singularity image for public use. Any feedback much appreciated.

Best, Dan

[fcamara7]

Hi Dan,

Thanks for your reply, I have passed the singularity image to our system administrators so that they can attempt to install the programs from it. I will get back to you on that.

I am also currently parsing the BAM file for only the chromosomes contained in the assembly. I will let you know how that goes.

Regards,

Francisco

On Sun, Oct 8, 2017 at 11:12 PM, Daniel Mapleson notifications@github.com wrote:

Hi Francisco,

Ah ok. So then it's likely that the discrepancy between the reference fasta and the BAM will likely explain your issue. You could use samtools to strip the BAM of any alignments to target sequences not in the reference.

I have just added a singularity image here: https://github.com/maplesond/portcullis/releases/download/Release-1.0.2/portcullis-1.0.2-singularity.img It contains two apps: portcullis and junctools. I'm keen to get some feedback on this as it's the first time I've built a singularity image for public use. Any feedback much appreciated.

Best, Dan

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[fcamara7]

Hi Dan,

I have managed to get portcullis to work on our cluster now (thanks!). Oddly we are still having problems with junctools though:

"/software/as/el7.2/EasyBuild/CRG/software/Python/3.6.1-foss-2017a/bin/python3: error while loading shared libraries: libpython3.6m.so.1.0: cannot open shared object file: No such file or directory"

As for the singularity, one of our system administrators tried to "unpack" it but got the following errors:

singularity -d shell /software/rg/el7.2/fcamara/ portcullis-1.0.2-singularity.img ...

VERBOSE [U=32002,P=47374] singularity_image_mount() Checking what kind of image we are mounting VERBOSE [U=32002,P=47374] singularity_image_mount() Attempting to mount as singularity image DEBUG [U=32002,P=47374] singularity_registry_get() Returning NULL on 'WRITABLE' DEBUG [U=32002,P=47374] singularity_priv_escalate() Temporarily escalating privileges (U=32002) DEBUG [U=0,P=47374] singularity_priv_escalate() Clearing supplementary GIDs. VERBOSE [U=0,P=47374] singularity_image_mount_image_mount() Mounting /dev/loop0 in read/only to: /var/singularity/mnt/container ERROR [U=0,P=47374] singularity_image_mount_image_mount() Failed to mount image in (read only): Invalid argument ABORT [U=0,P=47374] singularity_image_mount_image_mount() Retval = 255 Regards,

Francisco

On Mon, Oct 9, 2017 at 4:27 PM, Francisco Câmara Ferreira < francisco.camara@crg.es> wrote:

Hi Dan,

Thanks for your reply, I have passed the singularity image to our system administrators so that they can attempt to install the programs from it. I will get back to you on that.

I am also currently parsing the BAM file for only the chromosomes contained in the assembly. I will let you know how that goes.

Regards,

Francisco

On Sun, Oct 8, 2017 at 11:12 PM, Daniel Mapleson <notifications@github.com

wrote:

Hi Francisco,

Ah ok. So then it's likely that the discrepancy between the reference fasta and the BAM will likely explain your issue. You could use samtools to strip the BAM of any alignments to target sequences not in the reference.

I have just added a singularity image here: https://github.com/maplesond/ portcullis/releases/download/Release-1.0.2/portcullis-1.0. 2-singularity.img It contains two apps: portcullis and junctools. I'm keen to get some feedback on this as it's the first time I've built a singularity image for public use. Any feedback much appreciated.

Best, Dan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/maplesond/portcullis/issues/25#issuecomment-335038924, or mute the thread https://github.com/notifications/unsubscribe-auth/ARkGEUxBoMVfzXuNsvVZuNcS3U8LUviqks5sqTq7gaJpZM4Pwq3y .

[lucventurini]

Hi Francisco, the problem with junctools seems to be more a general problem of Python, from the error message. Can you execute any python3 code at all with /software/as/el7.2/EasyBuild/CRG/software/Python/3.6.1-foss-2017a/bin/python3? Could it be that Python3 has not been loaded correctly in your environment?

[fcamara7]

Hi Luca,

In fact yes, I think this is the version of python we load into the cluster environment and that allows us to run portcullis. Isn´t it right Luis?

Thanks,

Francisco

On Tue, Oct 10, 2017 at 3:33 PM, Luca Venturini notifications@github.com wrote:

Hi Francisco, the problem with junctools seems to be more a general problem of Python, from the error message. Can you execute any python3 code at all with /software/as/el7.2/EasyBuild/CRG/software/Python/3.6.1-foss-2017a/bin/python3? Could it be that Python3 has not been loaded correctly in your environment?

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[maplesond]

I think the issue maybe that you need the python development libraries for this to work correctly.

As for singularity, thanks for the feedback. I'll check this out later. Can you also try running the apps directly: singularity run portcullis-1.0.2-singularity.img portcullis <args>

[maplesond]

This installation issue is fixed in the current version V1.1.0.

[fcamara7]

Thanks for the info Daniel.

Cheers,

Francisco

On Mon, Mar 19, 2018 at 2:25 PM, Daniel Mapleson notifications@github.com wrote:

This installation issue is fixed in the current version V1.1.0.

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