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Vini2 / phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
https://phables.readthedocs.io/
MIT License
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Empty edges.fasta.frag.faa file despite correct input #49

Closed jonye123 closed 3 weeks ago

jonye123 commented 3 months ago

Hi, I am running into an error with scan_smg because it says that my edges.fasta.frag.faa file is empty. I am not sure why this is the case as my input file is properly formatted as gfa.

Vini2 commented 3 months ago

Hi @jonye123,

Thanks for your interest in Phables.

Can you please provide more details about the issue?

Thanks, Vijini

jonye123 commented 3 months ago

Hi Vijini,

Thanks for getting back to me so quickly! I am currently using version 1.3.1 and am running phables on a cyanophage genome I assembled using SPAdes. I've attached the requested files to this email as well. The error log (0 bytes) is empty so I am unable to attach it.

On Wed, Apr 10, 2024 at 11:31 PM Vijini Mallawaarachchi < @.***> wrote:

Hi @jonye123 https://github.com/jonye123,

Thanks for your interest in Phables.

Can you please provide more details about the issue?

  • What version of Phables are you using? You can get the version information using the command phables --version.
  • What type of data are you running phables on? (metagenome, virome or phage isolate)
  • Can you please share with me the log files logs/smg_scan_frag_err.log and log/smg_scan_frag_out.log? (you can drag and drop the files to the reply and they will attach).
  • If possible, can you please share with me the GFA file you are using?

Thanks, Vijini

— Reply to this email directly, view it on GitHub https://github.com/Vini2/phables/issues/49#issuecomment-2049009246, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOERVIWRYNOTSLNKXZBFFTY4YU4XAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBZGAYDSMRUGY . You are receiving this because you were mentioned.Message ID: @.***>

jonye123 commented 3 months ago

Hi Vijini,

Thanks for getting back to me so quickly! I am currently using version 1.3.1 and am running phables on a cyanophage genome I assembled using SPAdes. I'm unable to attach the gfa file here, so I've emailed it. smg_scan_frag_out.log smg_scan_frag_err.log

Vini2 commented 3 months ago

Hi @jonye123

Can you please let me know the specs of the machine you are using to run Phables (OS, version, etc.)?

Thanks, Vijini

jonye123 commented 3 months ago

Yes, I am using macOS 13.6.1 (22G313). The processor is a 1.2 GHz Dual-Core Intel Core m3. I currently have about 23 GB of storage available. Please let me know if you need any more information,

Thanks, Jon

On Thu, Apr 11, 2024 at 2:11 PM Vijini Mallawaarachchi < @.***> wrote:

Hi @jonye123 https://github.com/jonye123

Can you please let me know the specs of the machine you are using to run Phables (OS, version, etc.)?

Thanks, Vijini

— Reply to this email directly, view it on GitHub https://github.com/Vini2/phables/issues/49#issuecomment-2050558139, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOERVMVJX6GVDBIRHNJP6TY434BJAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJQGU2TQMJTHE . You are receiving this because you were mentioned.Message ID: @.***>

Vini2 commented 3 months ago

Hi @jonye123,

I believe macOS is the issue. Phables uses Fraggenescan to predict the genes in the sequences. I could not run Fraggenescan on macOS, only on Linux. I would suggest running Phables on a Linux machine.

I will make a note to replace Fraggenescan with probably Prodigal or pyrodigal.

Sorry about the inconvenience. Thanks for pointing out this issue.

Regards, Vijini

jonye123 commented 2 months ago

Thank you!

On Thu, Apr 11, 2024 at 6:54 PM Vijini Mallawaarachchi < @.***> wrote:

Hi @jonye123 https://github.com/jonye123,

I believe macOS is the issue. I could not run Fraggenescan on macOS, only on Linux. I would suggest running Phables on a Linux machine.

I will make a note to replace Fraggenescan with probably Prodigal or pyrodigal-gv.

Sorry about the inconvenience. Thanks for pointing out this issue.

Regards, Vijini

— Reply to this email directly, view it on GitHub https://github.com/Vini2/phables/issues/49#issuecomment-2050827852, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOERVNI2O7ENCR7HS6P2STY445G3AVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJQHAZDOOBVGI . You are receiving this because you were mentioned.Message ID: @.***>

jonye123 commented 2 months ago

Hi Vijini,

I tried running phables on a Linux virtual machine, however, I seem to still be running into the same problem. Do you have any other thoughts as to why this might be happening?

On Sun, Apr 14, 2024 at 5:37 PM Jon Ye @.***> wrote:

Thank you!

On Thu, Apr 11, 2024 at 6:54 PM Vijini Mallawaarachchi < @.***> wrote:

Hi @jonye123 https://github.com/jonye123,

I believe macOS is the issue. I could not run Fraggenescan on macOS, only on Linux. I would suggest running Phables on a Linux machine.

I will make a note to replace Fraggenescan with probably Prodigal or pyrodigal-gv.

Sorry about the inconvenience. Thanks for pointing out this issue.

Regards, Vijini

— Reply to this email directly, view it on GitHub https://github.com/Vini2/phables/issues/49#issuecomment-2050827852, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOERVNI2O7ENCR7HS6P2STY445G3AVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJQHAZDOOBVGI . You are receiving this because you were mentioned.Message ID: @.***>

Vini2 commented 2 months ago

Hi @jonye123,

That seems a bit strange. Can you please share with me your assembly graph file and edges file?

jonye123 commented 2 months ago

Sure, no problem.

On Wed, Apr 17, 2024 at 9:04 PM Vijini Mallawaarachchi < @.***> wrote:

Hi @jonye123 https://github.com/jonye123,

That seems a bit strange. Can you please share with me your assembly graph file and edges file?

— Reply to this email directly, view it on GitHub https://github.com/Vini2/phables/issues/49#issuecomment-2062949180, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOERVIZ6GIOJMCJDYODV5LY55A3RAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRSHE2DSMJYGA . You are receiving this because you were mentioned.Message ID: @.***>

Vini2 commented 2 months ago

Hi @jonye123,

Just checking if you sent me your assembly graph file and edges file.

Thanks!

jonye123 commented 2 months ago

Hi,

Yes I sent them a few days ago! Were you able to receive them?

On Mon, Apr 29, 2024 at 10:54 PM Vijini Mallawaarachchi < @.***> wrote:

Hi @jonye123 https://github.com/jonye123,

Just checking if you sent me your assembly graph file and edges file.

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/Vini2/phables/issues/49#issuecomment-2084434371, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOERVMJR7TMZSEL4O6UN7TY74WYHAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBUGQZTIMZXGE . You are receiving this because you were mentioned.Message ID: @.***>

Vini2 commented 2 months ago

Hi @jonye123,

No, I didn't get them. Did you email me?

jonye123 commented 2 months ago

Yes, I replied in this thread. It said it was sent on the 18th

On Mon, Apr 29, 2024 at 11:27 PM Vijini Mallawaarachchi < @.***> wrote:

Hi @jonye123 https://github.com/jonye123,

No, I didn't get them. Did you email me?

— Reply to this email directly, view it on GitHub https://github.com/Vini2/phables/issues/49#issuecomment-2084472757, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOERVND5QVOKGPDKKCUUDLY742VVAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBUGQ3TENZVG4 . You are receiving this because you were mentioned.Message ID: @.***>

Vini2 commented 2 months ago

Hi @jonye123,

Sorry, I haven't received the data. Can you upload it to Google Drive or DropBox and share it? Emailing might be a bit of an issue.

Thanks!

Vini2 commented 3 weeks ago

Hi @jonye123,

Sorry, it's been a while since you posted this issue. Was this issue fixed?

Can you please try the latest version of Phable (v1.3.3) and let me know if you still come across the error?

Thanks!

jonye123 commented 3 weeks ago

Hi Vijini,

I ended taking a different direction with my project. Apologies for not following up. I can take look at the updated version when I get the chance though. Thanks!

On Wed, Jun 12, 2024 at 11:33 PM Vijini Mallawaarachchi < @.***> wrote:

Hi @jonye123 https://github.com/jonye123,

Sorry, it's been a while since you posted this issue. Was this issue fixed?

Can you please try the latest version of Phable (v1.3.3) and let me know if you still come across the error?

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/Vini2/phables/issues/49#issuecomment-2164612795, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOERVMPCQRQ6B3PN32LERDZHE4MFAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRUGYYTENZZGU . You are receiving this because you were mentioned.Message ID: @.***>

Vini2 commented 3 weeks ago

Closing the issue for now. Please re-open if needed.