Comments (12)
SionBayliss
commented on June 30, 2024
1
HI Ignacio,
Sorry for not getting back to you sooner, this has been an insane few months for me. This method worked for me on the files you supplied. Are you sure that PIRATE is calling the appropriate file that you modified? Perhaps clone PIRATE, comment out the appropriate sections and then call that version of PIRATE using the full path to see if that works.
Again, sorry for the long time to reply.
All the best,
Sion
from pirate.
SionBayliss
commented on June 30, 2024
Hi Ignacio,
The _1 (or _integer) after a gene name means that the gene family is multicopy and has split into multiple gene families by PIRATE. Sometimes this is unsuitable for your analysis and can be switched off.
When PIRATE runs it initially tells you how many gffs have passed QC. Did your genome get to this stage?
All the best,
Sion
…________________________________
From: Ignacio Ferrés ***@***.***>
Sent: 23 June 2021 18:45
To: SionBayliss/PIRATE ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [SionBayliss/PIRATE] Missing genome in output (#70)
Hi, I have been trying PIRATE on simulated gffs and there's a genome which is missing in the final .tsvs files whereas they get into the initial steps of the workflow.
I attach here the PIRATE.gene_families.ordered.tsv output file (I change the extension to "csv" to comply with github formats, but it's the tsv). See the empty column for genome1.
PIRATE.gene_families.ordered.csv<https://github.com/SionBayliss/PIRATE/files/6704171/PIRATE.gene_families.ordered.csv>
I can provide you the simulated gff if you want to test it, or any log file.
Also, I would like to know what does the "(1)" suffix mean attached to some gene names.
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub<#70>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACXFVLGBTRFVNIMRYL4SV7TTUITSZANCNFSM47GLY33A>.
from pirate.
iferres
commented on June 30, 2024
Thanks Sion,
For what I see, genome1.gff appears to make it into the modified_gffs directory, and its structure looks fine, same as the rest of the genomes.
from pirate.
SionBayliss
commented on June 30, 2024
Hi Ignacio,
Do you want to send my ~3 genomes for me to do a test run on?
All the best,
Sion
…________________________________
From: Ignacio Ferrés ***@***.***>
Sent: 24 June 2021 11:18
To: SionBayliss/PIRATE ***@***.***>
Cc: Sion Bayliss ***@***.***>; Comment ***@***.***>
Subject: Re: [SionBayliss/PIRATE] Missing genome in output (#70)
Thanks Sion,
For what I see, genome1.gff appears to make it into the modified_gffs directory, and its structure looks fine, same as the rest of the genomes.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#70 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACXFVLHAHJ7YUWD6AHURU5LTUMIAVANCNFSM47GLY33A>.
from pirate.
iferres
commented on June 30, 2024
Here is the dataset where it fails, there're 10 simulated genomes. The gffs looks little weird because I needed to simulate one gene per contig, but PIRATE seems to cope with them except for a few.
from pirate.
SionBayliss
commented on June 30, 2024
Hi Ignacio,
It looks like PIRATE is filtering out all of the genes in genome1.
It is doing this during the feature extraction step. The filtering criteria are that a CDS must have a nucleotide length divisible by 3, <5% NS, a consensus start/stop codon and be >120 bp long. It might be worth checking to see if this is the case for your simulated genes in genome 1?
All the best,
Sion
…________________________________
From: Ignacio Ferrés ***@***.***>
Sent: 24 June 2021 12:35
To: SionBayliss/PIRATE ***@***.***>
Cc: Sion Bayliss ***@***.***>; Comment ***@***.***>
Subject: Re: [SionBayliss/PIRATE] Missing genome in output (#70)
Here is the dataset where it fails, there're 10 simulated genomes. The gffs looks little weird because I needed to simulate one gene per contig, but PIRATE seems to cope with them except for a few.
simulated_gffs.tar.gz<https://github.com/SionBayliss/PIRATE/files/6709168/simulated_gffs.tar.gz>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#70 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACXFVLHTEVYZNIKN2ZLGKPTTUMRAJANCNFSM47GLY33A>.
from pirate.
iferres
commented on June 30, 2024
Ok, yes. Apparently genome1 doesn't pass the filter. I checked and it's the only genome where any of its genes pass all of them. Is there any way to relax these filters? Many genes from the other genomes may be being filtered out as well.
Thanks for your time. Closing this.
from pirate.
SionBayliss
commented on June 30, 2024
Hi Ignacio,
You can uncomment/edit out the relevant lines in extract_feature_sequences.pl:
Gene length:
```
my $length_threshold = 120;
```
Triplicate reading frame (this won't make much sense if you are treating it like a CDS and will likely throw errors later in the pipeline):
```
# must be divisible by 3
if( ($l % 3) != 0 ){
$include = 0; <- this line
}
```
Consensus stop and start codons. You can also change the default expected codons earlier in the script:
```
# have consensus stop codon.
if ( ! $stop_codons{substr($seq, -3)} ){
$include = 0; <- this line
}
# have consensus start codon.
if ( ! $start_codons{substr($seq, 0, 3)} ){
$include = 0; <- this line
}
```
5% NS:
```
# have <5% Ns
if( ($ns/$l) > "0.05" ){ <- this value if you want to change the default proportions of N sites.
$include = 0; <- this line
}
```
Hope that helps,
Sion
…________________________________
From: Ignacio Ferrés ***@***.***>
Sent: 24 June 2021 20:18
To: SionBayliss/PIRATE ***@***.***>
Cc: Sion Bayliss ***@***.***>; Comment ***@***.***>
Subject: Re: [SionBayliss/PIRATE] Missing genome in output (#70)
Closed #70<#70>.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub<#70 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACXFVLEC255HZJJGJYDGSYLTUOHJ7ANCNFSM47GLY33A>.
from pirate.
iferres
commented on June 30, 2024
Thanks a lot Sion.
Bests,
Ignacio
from pirate.
iferres
commented on June 30, 2024
Hi Sion, hope you are doing well.
I removed the filters as you suggested but genome1.gff is still being filtered out.
Here's the extract_feature_sequences.pl script on my PIRATE's fork:
https://github.com/iferres/PIRATE/blob/master/scripts/extract_feature_sequences.pl
I tested the build with a Singularity container, I could provide the definition file if you are familiar with Singularity.
I digged into the code but couldn't find anything, I'm not a perl expert tho. I'd appreciate any other suggestion.
Bests!
from pirate.
iferres
commented on June 30, 2024
Sion, just to let you know that I read your last message, and sorry for not answering before. It's okay to me to close this issue since I don't know when am I going to address it. I will come back if I address it in the following months.
Bests!
from pirate.
SionBayliss
commented on June 30, 2024
Hi Ignacio,
No problem. If you get back to it please let me know and I will try and help however I can.
All the best,
Sion
…________________________________
From: Ignacio Ferrés ***@***.***>
Sent: 15 November 2021 12:46
To: SionBayliss/PIRATE ***@***.***>
Cc: Sion Bayliss ***@***.***>; State change ***@***.***>
Subject: Re: [SionBayliss/PIRATE] Missing genome in output (#70)
Sion, just to let you know that I read your last message, and sorry for not answering before. It's okay to me to close this issue since I don't know when am I going to address it. I will come back if I address it in the following months.
Bests!
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub<#70 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACXFVLEON3UMYZILADU742LUMD6LBANCNFSM47GLY33A>.
Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
from pirate.
Related Issues (20)
- extract_feature_sequences.pl failed HOT 2
- error observed during "aligning all feature sequences" HOT 2
- Output gene sequences to run gene alignment separately HOT 4
- PIRATE_plots.pdf created by plot_summary.R HOT 1
- Error after MCL clustering step HOT 5
- How do you tell which gene families are single-copy or multi-copy? HOT 2
- Feature request: Option to include original IDs and annotations in fasta headers for align_features_sequences script HOT 2
- Average_dose =1 is appropriate to determine whether a gene family is a single copy？ HOT 1
- - ERROR: link_clusters.pl failed. HOT 1
- Undefined subroutine &main::translate called HOT 2
- Error when running PIRATE MCL process
- For some single loci, a gene family but for others not. HOT 1
- problem in installation HOT 9
- Bump version in new release HOT 4
- Missing output files and coregenom files HOT 3
- Running on large dataset HOT 2
- stuck at threshold 60 during MCL clustering HOT 3
- PIRATE.pangenome_summary.txt HOT 6
- understanding pirate results
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pirate.