heche-psb
commented
2 years ago Hi Muthulakshmi,
I downloaded the enclosed file "sample.tar.gz" from you and reran the collinearity analysis successfully. Here is my step:
First, I reformat the gene ID of the CDS file "sample.fasta" to make it match the GFF file "ath.gff" in a python session:
>>>import pandas as pd
>>>df=pd.read_csv('sample.fasta',header=None)
>>>df2=df[0].astype(str).str.split(' | ',expand=True)
>>>df2[0].to_csv('sample.fa.cds',sep="\t",header=False, index=False)Now I got the reformatted CDS file "sample.fa.cds" for next step;
To infer paralogous gene family, I used command:
$wgd dmd sample.fa.cds
2022-09-16 13:28:04: ERROR Translation error (First codon 'TCA' is not a start codon) in seq AT1G03325.1
2022-09-16 13:28:04: ERROR Translation error (First codon 'AGG' is not a start codon) in seq AT1G04105.1
2022-09-16 13:28:05: ERROR Translation error (First codon 'AAT' is not a start codon) in seq AT1G13805.1
2022-09-16 13:28:05: ERROR Translation error (Sequence length 2351 is not a multiple of three) in seq AT1G17000.1
[...]
2022-09-16 13:28:13: ERROR Translation error (First codon 'ACG' is not a start codon) in seq ATMG01275.1
2022-09-16 13:28:13: ERROR Translation error (Sequence length 922 is not a multiple of three) in seq ATMG01320.1
2022-09-16 13:28:14: INFO One CDS file: will compute paranome##Note that there were quite some genes that couldn't be correctly translated.
And I got two files in the "wgd_dmd" directory, "sample.fa.cds.mcl" and "sample.fa.cds_sample.fa.cds.tsv";
Next I inferred the collinearity based on the freshly-gained gene family information (assumed that I was still in the same directory which contained the original data):
$wgd syn -f mRNA -a ID ath.gff wgd_dmd/sample.fa.cds.mcl
2022-09-16 13:34:28: INFO i-adhore stdout: This is i-ADHoRe v3.0.
Copyright (c) 2002-2010, Flanders Interuniversity Institute for Biotechnology, VIB.
Algorithm designed by Klaas Vandepoele, Cedric Simillion, Jan Fostier, Dieter De Witte,
Koen Janssens, Sebastian Proost, Yvan Saeys and Yves Van de Peer.
Process 1/1 is alive on localhost.
2022-09-16 13:34:28: INFO i-adhore stderr: Error opening the settings file: -version
2022-09-16 13:34:28: INFO Made output directory ./wgd_syn
2022-09-16 13:34:28: INFO Parsing GFF file
2022-09-16 13:34:30: INFO Writing gene lists
2022-09-16 13:34:30: INFO Writing families file
2022-09-16 13:34:30: INFO Writing configuration file
2022-09-16 13:34:30: INFO Running I-ADHoRe 3.0
2022-09-16 13:35:03: WARNING WARNING: Maximum allowed number of gaps in the alignment not specified. Setting to cluster_gap.
WARNING: Tandem gap size not correct in settings file. Using default (gap_size / 2)
2022-09-16 13:35:03: INFO
This is i-ADHoRe v3.0.
Copyright (c) 2002-2010, Flanders Interuniversity Institute for Biotechnology, VIB.
Algorithm designed by Klaas Vandepoele, Cedric Simillion, Jan Fostier, Dieter De Witte,
Koen Janssens, Sebastian Proost, Yvan Saeys and Yves Van de Peer.
Process 1/1 is alive on localhost.
************* i-ADHoRe parameters *************
Number of genelists = 7
Blast table = ./wgd_syn/families.tsv
Output path = ./wgd_syn/i-adhore-out/
Gap size = 30
Cluster gap size = 35
Cloud gap size = 0
Cloud cluster gap size = 0
Max gaps in alignment = 35
Tandem gap = 15
Flush output = 1000
Q-value = 0.75
Anchorpoints = 3
Probability cutoff = 0.01
Cloud filtering method = Binomial
Level 2 only = false
Use family = true
Write statistics = false
Alignment method = GreedyGraphbased4
Multiple hypothesis correction = FDR
Number of threads = 1
Compare aligners = false
Collinear searches only
Visualize GHM.png = false
Visualize Alignment = true
Verbose output = true
************ END i-AdDHoRe parameters *********
Creating dataset... done. (time: 0.022624s)
Mapping gene families... done. (time: 0.031497s)
Remapping tandem duplicates... done. (time: 0.0159261s)
Writing genelists file... done. (time: 0.113681s)
Collinear Search
Level 2 multiplicon detection... done. (time: 1.72764s)
Profile detection...
433 multiplicons to evaluate - evaluating level 2 multiplicon... 25 new multiplicons found.
[...]
2 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
1 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
Flushing output files...Visualize AlignedProfiles
badprofile (all boxes will be black! => segmentlength differs among the segs of alignment)
badprofile (all boxes will be black! => segmentlength differs among the segs of alignment)
done.
Time for Higher Level Detection: 30.8817s.
All Done! Bye...
2022-09-16 13:35:03: INFO Drawing co-linearity dotplot
2022-09-16 13:35:11: INFO Done
The resulting file "sample.fa.cds.mcl.dotplot.svg" in directory "wgd_syn" is the inferred intraspecific collinear dotplot, as shown below.
Given the successful run of "wgd syn" without Ks data, I suppose it will also be no problem for another run with Ks data. It's weird that your result file "sample.fasta.blast.tsv.mcl.dotplot" was even empty. Do you have the log file of that failed run, we can diagnose further in detail based on that log.
muthu1722
lizhao007
Hi, I have used supplementary material to run WGD. I am able to rum till wgd syn without any issue but in the wgd_syn results only dotplot as well as ks_ancjors.tsv files are empty. I have also tried with one sample data just to confirm whether the data am using creating any trouble but again with sample data I have got the same issue but other than these two files my histogram, tsv.mcl files are looking fine for both sample data and my own data. I am attaching my sample data as well as output for your refernce. It would be really helpful if you could help me to resolve it . Thank you in advance. Muthulakshmi sample.tar.gz