Empty edges.fasta.frag.faa file despite correct input #49
Comments
|
Hi @jonye123, Thanks for your interest in Phables. Can you please provide more details about the issue?
Thanks, |
|
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
<#49 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AVOERVIWRYNOTSLNKXZBFFTY4YU4XAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBZGAYDSMRUGY>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
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. |
|
Hi @jonye123 Can you please let me know the specs of the machine you are using to run Phables (OS, version, etc.)? Thanks, |
|
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
<#49 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AVOERVMVJX6GVDBIRHNJP6TY434BJAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJQGU2TQMJTHE>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
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, |
|
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
<#49 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AVOERVNI2O7ENCR7HS6P2STY445G3AVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJQHAZDOOBVGI>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
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
> <#49 (comment)>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AVOERVNI2O7ENCR7HS6P2STY445G3AVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJQHAZDOOBVGI>
> .
> You are receiving this because you were mentioned.Message ID:
> ***@***.***>
>
|
|
Hi @jonye123, That seems a bit strange. Can you please share with me your assembly graph file and edges file? |
|
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
<#49 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AVOERVIZ6GIOJMCJDYODV5LY55A3RAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRSHE2DSMJYGA>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
Hi @jonye123, Just checking if you sent me your assembly graph file and edges file. Thanks! |
|
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
<#49 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AVOERVMJR7TMZSEL4O6UN7TY74WYHAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBUGQZTIMZXGE>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
Hi @jonye123, No, I didn't get them. Did you email me? |
|
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
<#49 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AVOERVND5QVOKGPDKKCUUDLY742VVAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBUGQ3TENZVG4>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
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! |
|
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! |
|
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
<#49 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AVOERVMPCQRQ6B3PN32LERDZHE4MFAVCNFSM6AAAAABGBHYPMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRUGYYTENZZGU>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
Closing the issue for now. Please re-open if needed. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
The text was updated successfully, but these errors were encountered: