Some output files missing or empty.

[drabe004]

Hi there... I've run this program on ~21k orthogroups (seq+trees) and I'm seeing that about 1900 output files are empty, and ~3000 did not produce an input file.

I picked a few of these out individually, and both times they replicated the results.

I can't quite work out what is happening here, perhaps these are non-resolvable?

Can you provide any insight as to why this would happen?

[drabe004]

I mean did not produce an output file

[JLSteenwyk]

Hi @drabe004,

Thank you for using OrthoSNAP!

Can you provide some input files and let me know what version of OrthoSNAP you are using?

best,

Jacob

[drabe004]

OG0000005tree.txt OG0000005seq.txt Sure-- these two files (changed from fa and tre format to be able to attach here) do not produce an output file.

[drabe004]

And these two: OG0000013tree.txt OG0000013seq.txt

Produce a blank output file.

I just installed this a couple days ago, so I'm assuming I'm using the latest version

[JLSteenwyk]

Sounds good - thank you. But can you let me know the specific version? You can see it in the help message

[drabe004]

Hi!

Sorry I just saw this in my email

version = "1.0.0"

On Wed, Jun 28, 2023 at 11:38 PM Jacob L. Steenwyk @.***> wrote:

Sounds good - thank you. But can you let me know the specific version? You can see it in the help message

— Reply to this email directly, view it on GitHub https://github.com/JLSteenwyk/orthosnap/issues/6#issuecomment-1612419389, or unsubscribe https://github.com/notifications/unsubscribe-auth/APEQMAHW6IFOFRCUDDEU7VTXNUBF7ANCNFSM6AAAAAAZXNVOMU . You are receiving this because you were mentioned.Message ID: @.***>

-- Danielle H Drabeck PhD Postdoctoral Fellow

Department of Ecology, Evolution, and BehaviorUniversity of Minnesota

@. @. Pronouns: She/Her/Hers

[JLSteenwyk]

Hi, I am running the test files, but they are rather large and take a long time to run. Would you happen to have an example file that runs faster?

Ideally, an example that identified SNAP-OG(s) but ran within 10 seconds.

Can you also provide the command you used?

[JLSteenwyk]

Hi, looping back to this

[drabe004]

Hi Jacob,

Apologies, my kids are home for the holiday so I haven’t had a moment to sort through to see if there are smaller files that produce 0 output. We’re running these on a cluster so they run pretty quickly on there, is that an option? In either case I’ll sift through the files tomorrow and try to find smaller ones.

Thanks for following up!

On Mon, Jul 3, 2023 at 10:25 PM Jacob L. Steenwyk @.***> wrote:

Hi, looping back to this

— Reply to this email directly, view it on GitHub https://github.com/JLSteenwyk/orthosnap/issues/6#issuecomment-1619414017, or unsubscribe https://github.com/notifications/unsubscribe-auth/APEQMAHNX43ZSKNIAOQWIS3XOOELXANCNFSM6AAAAAAZXNVOMU . You are receiving this because you were mentioned.Message ID: @.***>

-- Danielle H Drabeck PhD Postdoctoral Fellow

Department of Ecology, Evolution, and BehaviorUniversity of Minnesota

@. @. Pronouns: She/Her/Hers

[JLSteenwyk]

Hi,

Looping back to this.

[drabe004]

Hi!

Apologies for the lack of reply--- I has sort of put this project aside for a week.

I am looking for smaller files but unfortunately.. this dataset is large and all the files (trees/seqs) include about the same number of species.

Is there anyway to trouble shoot this on a cluster ?

Alternatively, I could give you an S3 link to all of the input files that resulted in an empty file, or a missing file.

Would either of those work?

Thanks so much,

~Danielle

On Tue, Jul 11, 2023 at 12:07 PM Jacob L. Steenwyk @.***> wrote:

Hi,

Looping back to this.

— Reply to this email directly, view it on GitHub https://github.com/JLSteenwyk/orthosnap/issues/6#issuecomment-1631184002, or unsubscribe https://github.com/notifications/unsubscribe-auth/APEQMAEOGQQLBZOXSMORFJDXPWB4RANCNFSM6AAAAAAZXNVOMU . You are receiving this because you were mentioned.Message ID: @.***>

-- Danielle H Drabeck PhD Postdoctoral Fellow

Department of Ecology, Evolution, and BehaviorUniversity of Minnesota

@. @. Pronouns: She/Her/Hers

[drabe004]

Oh! I just found a small input file that resulted in an empty output!

See attached!

On Thu, Jul 13, 2023 at 9:37 AM Danielle Drabeck @.***> wrote:

Hi!

Apologies for the lack of reply--- I has sort of put this project aside for a week.

I am looking for smaller files but unfortunately.. this dataset is large and all the files (trees/seqs) include about the same number of species.

Is there anyway to trouble shoot this on a cluster ?

Alternatively, I could give you an S3 link to all of the input files that resulted in an empty file, or a missing file.

Would either of those work?

Thanks so much,

~Danielle

On Tue, Jul 11, 2023 at 12:07 PM Jacob L. Steenwyk < @.***> wrote:

Hi,

Looping back to this.

— Reply to this email directly, view it on GitHub https://github.com/JLSteenwyk/orthosnap/issues/6#issuecomment-1631184002, or unsubscribe https://github.com/notifications/unsubscribe-auth/APEQMAEOGQQLBZOXSMORFJDXPWB4RANCNFSM6AAAAAAZXNVOMU . You are receiving this because you were mentioned.Message ID: @.***>

-- Danielle H Drabeck PhD Postdoctoral Fellow

Department of Ecology, Evolution, and BehaviorUniversity of Minnesota

@. @. Pronouns: She/Her/Hers

-- Danielle H Drabeck PhD Postdoctoral Fellow

Department of Ecology, Evolution, and BehaviorUniversity of Minnesota

@. @. Pronouns: She/Her/Hers

[JLSteenwyk]

Hi Danielle,

There is no attachment in the previous comment.

best,

Jacob

[JLSteenwyk]

Hi,

I haven't received any more news about this issue. I am therefore going to close it.

Please feel free to write again.

best,

Jacob