fatal IO error 2 (No such file or directory)

[Johnsonzcode]

Dear Likui, Thank you for your tools. It's a new method to integrate multiple level information of HiFi reads. When I came to step ovlp2graph.py. It throwed an error.

XIO:  fatal IO error 2 (No such file or directory) on X server "localhost:14.0"
      after 29 requests (27 known processed) with 0 events remaining.
XIO:  fatal IO error 2 (No such file or directory) on X server "localhost:14.0"
      after 29 requests (27 known processed) with 0 events remaining.
XIO:  fatal IO error 2 (No such file or directory) on X server "localhost:14.0"
      after 29 requests (27 known processed) with 0 events remaining.

My command line is

ovlp2graph.py --overlap-file pga_best10.paf
# pga_best10.paf is from step 2

Sincerely Johnsonz

[matthew-pumc]

Hi @Johnsonzcode , I encountered an error like this, add a line of shebang at the first line of ovlp2graph.py could solve this error.

#!/usr/bin/env python

best, Matthew

FYI, the error info is:

import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
...
ovlp2graph.py: line 10: syntax error near unexpected token `('
ovlp2graph.py: line 10: `class OrderedSet(collections.abc.MutableSet):'

[Johnsonzcode]

Hi @matthew-pumc , Thank you so much, I will try by your information.

best, Johnsonz

[matthew-pumc]

Hi @Johnsonzcodehttps://github.com/Johnsonzcode, If you have read the help of the last step, the script will remind you that you should use the chr_paths as:

--chr-paths-fn chr_paths

I think the parameter descripted in readme is inconsistent with what is need by the scripts.

best, Matthew

On Nov 21, 2022, at 12:15, johnsonz @.***> wrote:

Hi @matthew-pumchttps://github.com/matthew-pumc , Your way is woking good. But the last step which file should I choose as --ctg-paths-fn, there are two ctg path file.

sg_edges_list chimers_nodes chr_paths ctg_paths ctgpath

best, Johnsonz

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[Johnsonzcode]

Thank your for your kind help. Yes, I found this option in scripts. I am waiting for the results.

[Johnsonzcode]

Dear @matthew-pumc , The result p_ctg.fasta seems not the final chrmosome. How could I get final chromosome ? best, Johnsonz

[matthew-pumc]

Hi Johnsonz, I’m afraid this result is the final chromosome, and I got a decent assembly in this file.

Best Matthew

From: @.> Sent: Monday, November 21, 2022 5:07 PM To: @.> Cc: Sijie @.>; @.> Subject: Re: [likui345/PGA] fatal IO error 2 (No such file or directory) (Issue #3)

Dear @matthew-pumchttps://github.com/matthew-pumc , The result p_ctg.fasta seems not the final chrmosome. How could I get final chromosome ? best, Johnsonz

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[Johnsonzcode]

Dear @matthew-pumc , How you tune the parameter, such as --best-n, minimum initial contigs length? best, Johnsonz

[matthew-pumc]

Hi Johnsonz, I did not tried my own data, I just used the data from this author’s article and set –best-n to 5 Then I have 12 chromosomes. I am going to use my own data this week, hope that I can get a great result.

Best, Matthew

From: @.> Sent: Tuesday, November 22, 2022 9:49 AM To: @.> Cc: Sijie @.>; @.> Subject: Re: [likui345/PGA] fatal IO error 2 (No such file or directory) (Issue #3)

Dear @matthew-pumchttps://github.com/matthew-pumc , How you tune the parameter, such as --best-n, minimum initial contigs length? best, Johnsonz

— Reply to this email directly, view it on GitHubhttps://github.com/likui345/PGA/issues/3#issuecomment-1322899296, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHCHIDIVOMUTKD7MCMAM5ZLWJQRC5ANCNFSM6AAAAAASFT3TTE. You are receiving this because you were mentioned.Message ID: @.***>

[Johnsonzcode]

Hi @matthew-pumc ,

Testing from article data is a good way. Hope you I can get a great result. BTW, what your data type? Only HiFi data ?

best, Johnsonz

[Johnsonzcode]

Hi @matthew-pumc , Actually, I got several decent chromosome from PGA, but not every chromosome. It is Exciting. Do you have wechat or something like that, maybe we can communicate assembly method on wechat?

[matthew-pumc]

you can search my id: matthew_hawking