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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
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epic2 with bedpe input issue #61

Open yussufhajjaj opened 2 years ago

yussufhajjaj commented 2 years ago

Hello!

I am trying to call peaks from H3K27me3 ChIPseq data, I converted the bams to bedpe as it is suggested for paired-end datasets. I get this error message:

"terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted"

command used: epic2 --treatment t.bedpe --control c.bedpe --chromsizes hg38_sizes.txt -fdr 0.01 --output mydir/file

Unfortunately, I cannot share the data, could you please help me with this?

Thanks in advance.

Yussuf

endrebak commented 2 years ago

Without the data it'd be too hard. Could you try to anonymize the data in some way or create a minimal reproducible example?

Does it happen on some of your non-confidential data?

yussufhajjaj commented 2 years ago

Hello,

Thanks for the reply, I created data for chr1 only, both conditions control and treatment, please find them through this link : https://drive.google.com/drive/u/0/folders/1Mm0q1xKIQfKttNpEG5k5Z79JILqtghOA

yussufhajjaj commented 2 years ago

Hi Endre,

Hope you good.

The error message only appears with the bedpe input, I used epic2 on my bam files and it works, but again not the suggested file format for Paired end data.

The same error message appear when I use your provided examples, and I really cannot understand the problem, and I hope you could help. Thanks in advance.

Yussuf

endrebak commented 2 years ago

I cannot help without any data to reproduce the error :) Many others have used the bedpe flag without issue so I'm 99% sure the issue is with the data being in an unexpected format.

On Fri, Jul 1, 2022 at 3:00 PM yussufhajjaj @.***> wrote:

Hi Endre,

Hope you good.

The error message only appears with the bedpe input, I used epic2 on my bam files and it works, but again not the suggested file format for Paired end data.

The same error message appear when I use your provided examples, and I really cannot understand the problem, and I hope you could help. Thanks in advance.

Yussuf

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yussufhajjaj commented 2 years ago

Oh sorry, are you facing a problem accessing the google drive link I provided above?

endrebak commented 2 years ago

Oh, sorry I did not see that link. In the first message you said you could not share the data.

I'll look at it next week :D

On Fri, Jul 1, 2022 at 3:31 PM yussufhajjaj @.***> wrote:

Oh sorry, are you facing a problem accessing the google drive link I provided above?

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endrebak commented 2 years ago

I'll need a linux machine to debug it. I'll have to put this issue on hold until I get access to a server with linux.

However, you could turn the bedpe into a bed where the interval is the midpoint between the two mate pairs and it would work with the regular epic2

On Fri, Jul 1, 2022 at 5:14 PM Endre Bakken Stovner @.***> wrote:

Oh, sorry I did not see that link. In the first message you said you could not share the data.

I'll look at it next week :D

On Fri, Jul 1, 2022 at 3:31 PM yussufhajjaj @.***> wrote:

Oh sorry, are you facing a problem accessing the google drive link I provided above?

— Reply to this email directly, view it on GitHub https://github.com/biocore-ntnu/epic2/issues/61#issuecomment-1172353393, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEHURUWLF62LWOGDIT756A3VR3XL5ANCNFSM5YGCB3YQ . You are receiving this because you commented.Message ID: @.***>

yussufhajjaj commented 2 years ago

Thanks for checking. Okay, I will be waiting for that.

But is that the format you mean or what? Or I miss understood sth, from this: chr9 123172513 123172563 chr9 123172652 123172698 39V34V1:121:C3V68ACXX:4:1101:1247:9184 42 + -

To this: chr9 123172563 123172652 39V34V1:121:C3V68ACXX:4:1101:1247:9184 42 +

endrebak commented 2 years ago

You can find the midpoint between the start and the end.

start + (end - start)/2 123172513 + (123172698 - 123172513)/2 = 123 172 605

So your interval is 123 172 605, 123 172 606

On Tue, Jul 5, 2022 at 5:29 PM yussufhajjaj @.***> wrote:

Thanks for checking. Okay, I will be waiting for that.

But is that the format you mean or what? Or I miss understood sth, from this: chr9 123172513 123172563 chr9 123172652 123172698 39V34V1:121:C3V68ACXX:4:1101:1247:9184 42 + -

To this: chr9 123172563 123172652 39V34V1:121:C3V68ACXX:4:1101:1247:9184 42 +

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yussufhajjaj commented 2 years ago

Even with a .bed file, using the midpoint, the same error message appear "terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted"

if I use the paired end bam, and put the --guess-bampe it says that it is an unused argument.

Mind that I installed epic2 from bioconda, maybe there is a version issue?

endrebak commented 2 years ago

I do not know, unfortunately. I will look into it when I get a linux machine or access to a linux server :D

On Tue, Jul 12, 2022 at 4:22 PM yussufhajjaj @.***> wrote:

Even with a .bed file, using the midpoint, the same error message appear "terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted"

if I use the paired end bam, and put the --guess-bampe it says that it is an unused argument.

Mind that I installed epic2 from bioconda, maybe there is a version issue?

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rogeroria commented 1 year ago

Hi there!

Has this issue being solved? It's happening to me.

Thanks for your help!

Roger

endrebak commented 1 year ago

i need data that reproduces the bug ☺️ Hard to debug otherwise

On Sun, 10 Sep 2023 at 03:23, rogeroria @.***> wrote:

Hi there!

Has this issue being solved? It's happening to me.

Thanks for your help!

Roger

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rogeroria commented 1 year ago

Hi!

Thank you for your quick response. I just sent you through WeTransfer two files (one of them used as a treatment and another as a control). Let me know if you can download them. (you should get an email in your gmail address).

Thank you again!

Roger

rogeroria commented 1 year ago

Hi Endrebak,

Where you able to download the data?

Thank you for your help.

Roger