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estebanpw / chromeister

A dotplot generator for large chromosomes
GNU General Public License v3.0
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error cannot open file 'dotplot.mat.csv': No such file or directory #3

Closed XuewenWangUGA closed 2 years ago

XuewenWangUGA commented 4 years ago

$scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000

output: 7.7M dotplot.mat

error: $ Rscript $scriptdir/compute_score.R dotplot.mat 2000 Error in file(con, "r") : cannot open the connection Calls: unlist -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file 'dotplot.mat.csv': No such file or directory Execution halted

it seems that the output "dotplot.mat.csv " is missing

estebanpw commented 4 years ago

Thanks for reporting this. The grid update introduced an error which was only apparent if the -dimension parameter was used. It should be now fixed.

Please update your repository using "git pull origin", then compile the files again with "make all" within the /src folder and rerun your experiment.

As a sidenote, also remember that if your input FASTA sequence is a multifasta containing more than ~50 sequences, then you should used the alternative script:

Rscript $scriptdir/compute_score-nogrid.R dotplot.mat 2000

XuewenWangUGA commented 4 years ago

Thank you for your updating and fixing the issue. I have downloaded the bin and run a test. It still has the same type of issue.

My testing data has only one seq in each input file. One sequence is around 100 Mbp and the other is around 95Mbp. I tested the tool on Ubuntu 18.04. It seems that the .csv output file is missing. my scripts: scriptdir=/home/xuewen/Downloads/chromeister-master/bin $scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000 && Rscript $scriptdir/compute_score.R dotplot.mat 2000

Do you have any suggestions on this? Thanks.

Xuewen

Xuewen

From: Esteban notifications@github.com Sent: Thursday, May 28, 2020 3:30 AM To: estebanpw/chromeister chromeister@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Thanks for reporting this. The grid update introduced an error which was only apparent if the -dimension parameter was used. It should be now fixed.

Please update your repository using "git pull origin", then compile the files again with "make all" within the /src folder and rerun your experiment.

As a sidenote, also remember that if your input FASTA sequence is a multifasta containing more than ~50 sequences, then you should used the alternative script:

Rscript $scriptdir/compute_score-nogrid.R dotplot.mat 2000

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/estebanpw/chromeister/issues/3#issuecomment-635164520, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGHDDYI2VUYXSVNHTSP3I5DRTYHJDANCNFSM4NMXSSSA.

XuewenWangUGA commented 4 years ago

The dotplot.mat file is generated but file "dotplot.mat.csv" is missing.

Here is the error information:

Error in file(con, "r") : cannot open the connection Calls: unlist -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file 'dotplot.mat.csv': No such file or directory Execution halted

Xuewen

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 12:36 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

Thank you for your updating and fixing the issue. I have downloaded the bin and run a test. It still has the same type of issue.

My testing data has only one seq in each input file. One sequence is around 100 Mbp and the other is around 95Mbp. I tested the tool on Ubuntu 18.04. It seems that the .csv output file is missing. my scripts: scriptdir=/home/xuewen/Downloads/chromeister-master/bin $scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000 && Rscript $scriptdir/compute_score.R dotplot.mat 2000

Do you have any suggestions on this? Thanks.

Xuewen

Xuewen

From: Esteban notifications@github.com Sent: Thursday, May 28, 2020 3:30 AM To: estebanpw/chromeister chromeister@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Thanks for reporting this. The grid update introduced an error which was only apparent if the -dimension parameter was used. It should be now fixed.

Please update your repository using "git pull origin", then compile the files again with "make all" within the /src folder and rerun your experiment.

As a sidenote, also remember that if your input FASTA sequence is a multifasta containing more than ~50 sequences, then you should used the alternative script:

Rscript $scriptdir/compute_score-nogrid.R dotplot.mat 2000

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/estebanpw/chromeister/issues/3#issuecomment-635164520, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGHDDYI2VUYXSVNHTSP3I5DRTYHJDANCNFSM4NMXSSSA.

XuewenWangUGA commented 4 years ago

scriptdir=/home/xuewen/Downloads/chromeister-master/bin $scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000 && Rscript $scriptdir/compute_score.R dotplot.mat 2000

more detailed log from above command:

[INFO] Loading database [INFO] Database loaded and of length 93964718. Hash table building took 1.422648e+01 seconds [INFO] Generating hits [INFO] Ratios: Q [5.574391e+04] D [4.698236e+04]. Lenghts: Q [111487820] D [93964718] 11%..21%..31%..41%..51%..61%..71%..81%..91%.. [INFO] Query length 110111402. Hits completed. Took 2.596973e+03 seconds [INFO] Writing matrix Error in file(con, "r") : cannot open the connection Calls: unlist -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file 'dotplot.mat.csv': No such file or directory Execution halted

Xuewen Wang, PhD

University of Georgia

email: xwwang@uga.edu

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 12:46 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

The dotplot.mat file is generated but file "dotplot.mat.csv" is missing.

Here is the error information:

Error in file(con, "r") : cannot open the connection Calls: unlist -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file 'dotplot.mat.csv': No such file or directory Execution halted

Xuewen

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 12:36 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

Thank you for your updating and fixing the issue. I have downloaded the bin and run a test. It still has the same type of issue.

My testing data has only one seq in each input file. One sequence is around 100 Mbp and the other is around 95Mbp. I tested the tool on Ubuntu 18.04. It seems that the .csv output file is missing. my scripts: scriptdir=/home/xuewen/Downloads/chromeister-master/bin $scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000 && Rscript $scriptdir/compute_score.R dotplot.mat 2000

Do you have any suggestions on this? Thanks.

Xuewen

Xuewen

From: Esteban notifications@github.com Sent: Thursday, May 28, 2020 3:30 AM To: estebanpw/chromeister chromeister@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Thanks for reporting this. The grid update introduced an error which was only apparent if the -dimension parameter was used. It should be now fixed.

Please update your repository using "git pull origin", then compile the files again with "make all" within the /src folder and rerun your experiment.

As a sidenote, also remember that if your input FASTA sequence is a multifasta containing more than ~50 sequences, then you should used the alternative script:

Rscript $scriptdir/compute_score-nogrid.R dotplot.mat 2000

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/estebanpw/chromeister/issues/3#issuecomment-635164520, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGHDDYI2VUYXSVNHTSP3I5DRTYHJDANCNFSM4NMXSSSA.

XuewenWangUGA commented 4 years ago

Esteban,

Finally I made it work. Thanks. I downloaded and recompiled the src.

Xuewen Wang, PhD

University of Georgia

email: xwwang@uga.edu

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 4:21 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

scriptdir=/home/xuewen/Downloads/chromeister-master/bin $scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000 && Rscript $scriptdir/compute_score.R dotplot.mat 2000

more detailed log from above command:

[INFO] Loading database [INFO] Database loaded and of length 93964718. Hash table building took 1.422648e+01 seconds [INFO] Generating hits [INFO] Ratios: Q [5.574391e+04] D [4.698236e+04]. Lenghts: Q [111487820] D [93964718] 11%..21%..31%..41%..51%..61%..71%..81%..91%.. [INFO] Query length 110111402. Hits completed. Took 2.596973e+03 seconds [INFO] Writing matrix Error in file(con, "r") : cannot open the connection Calls: unlist -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file 'dotplot.mat.csv': No such file or directory Execution halted

Xuewen Wang, PhD

University of Georgia

email: xwwang@uga.edu

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 12:46 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

The dotplot.mat file is generated but file "dotplot.mat.csv" is missing.

Here is the error information:

Error in file(con, "r") : cannot open the connection Calls: unlist -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file 'dotplot.mat.csv': No such file or directory Execution halted

Xuewen

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 12:36 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

Thank you for your updating and fixing the issue. I have downloaded the bin and run a test. It still has the same type of issue.

My testing data has only one seq in each input file. One sequence is around 100 Mbp and the other is around 95Mbp. I tested the tool on Ubuntu 18.04. It seems that the .csv output file is missing. my scripts: scriptdir=/home/xuewen/Downloads/chromeister-master/bin $scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000 && Rscript $scriptdir/compute_score.R dotplot.mat 2000

Do you have any suggestions on this? Thanks.

Xuewen

Xuewen

From: Esteban notifications@github.com Sent: Thursday, May 28, 2020 3:30 AM To: estebanpw/chromeister chromeister@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Thanks for reporting this. The grid update introduced an error which was only apparent if the -dimension parameter was used. It should be now fixed.

Please update your repository using "git pull origin", then compile the files again with "make all" within the /src folder and rerun your experiment.

As a sidenote, also remember that if your input FASTA sequence is a multifasta containing more than ~50 sequences, then you should used the alternative script:

Rscript $scriptdir/compute_score-nogrid.R dotplot.mat 2000

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/estebanpw/chromeister/issues/3#issuecomment-635164520, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGHDDYI2VUYXSVNHTSP3I5DRTYHJDANCNFSM4NMXSSSA.

XuewenWangUGA commented 4 years ago

Estebapw,

I have one question for you on how to understand the coordinate file "master.csv" Is the xStart, yStart the position (bp) in the sequence or the position in the plot?

Here is the first several lines of "master.csv"

Type,xStart,yStart,xEnd,yEnd,strand(f/r),block,length,score,ident,similarity,%ident,SeqX,SeqY Frag,121889,350742,122027,350880,f,0,139,500,132,89.93,0.95,0,0 Frag,322460,528543,322600,528683,f,0,141,468,129,82.98,0.91,0,0 Frag,326298,532332,327156,533190,f,0,859,2772,776,80.68,0.90,0,0 Frag,4431,109033,4638,109240,f,0,208,704,192,84.62,0.92,0,0 Frag,311,104565,538,104792,f,0,228,768,210,84.21,0.92,0,0

Thanks.

Xuewen Wang, PhD

University of Georgia

email: xwwang@uga.edu

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 5:19 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

Esteban,

Finally I made it work. Thanks. I downloaded and recompiled the src.

Xuewen Wang, PhD

University of Georgia

email: xwwang@uga.edu

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 4:21 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

scriptdir=/home/xuewen/Downloads/chromeister-master/bin $scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000 && Rscript $scriptdir/compute_score.R dotplot.mat 2000

more detailed log from above command:

[INFO] Loading database [INFO] Database loaded and of length 93964718. Hash table building took 1.422648e+01 seconds [INFO] Generating hits [INFO] Ratios: Q [5.574391e+04] D [4.698236e+04]. Lenghts: Q [111487820] D [93964718] 11%..21%..31%..41%..51%..61%..71%..81%..91%.. [INFO] Query length 110111402. Hits completed. Took 2.596973e+03 seconds [INFO] Writing matrix Error in file(con, "r") : cannot open the connection Calls: unlist -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file 'dotplot.mat.csv': No such file or directory Execution halted

Xuewen Wang, PhD

University of Georgia

email: xwwang@uga.edu

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 12:46 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

The dotplot.mat file is generated but file "dotplot.mat.csv" is missing.

Here is the error information:

Error in file(con, "r") : cannot open the connection Calls: unlist -> readLines -> file In addition: Warning message: In file(con, "r") : cannot open file 'dotplot.mat.csv': No such file or directory Execution halted

Xuewen

From: Xuewen Wang xwwang@uga.edu Sent: Thursday, May 28, 2020 12:36 PM To: estebanpw/chromeister chromeister@noreply.github.com; estebanpw/chromeister reply@reply.github.com Cc: Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

Thank you for your updating and fixing the issue. I have downloaded the bin and run a test. It still has the same type of issue.

My testing data has only one seq in each input file. One sequence is around 100 Mbp and the other is around 95Mbp. I tested the tool on Ubuntu 18.04. It seems that the .csv output file is missing. my scripts: scriptdir=/home/xuewen/Downloads/chromeister-master/bin $scriptdir/CHROMEISTER -query aradu.K30065.gnm1.chr01.fa -db aradu.K30060.gnm1.chr01.fa -out dotplot.mat -dimension 2000 && Rscript $scriptdir/compute_score.R dotplot.mat 2000

Do you have any suggestions on this? Thanks.

Xuewen

Xuewen

From: Esteban notifications@github.com Sent: Thursday, May 28, 2020 3:30 AM To: estebanpw/chromeister chromeister@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Thanks for reporting this. The grid update introduced an error which was only apparent if the -dimension parameter was used. It should be now fixed.

Please update your repository using "git pull origin", then compile the files again with "make all" within the /src folder and rerun your experiment.

As a sidenote, also remember that if your input FASTA sequence is a multifasta containing more than ~50 sequences, then you should used the alternative script:

Rscript $scriptdir/compute_score-nogrid.R dotplot.mat 2000

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/estebanpw/chromeister/issues/3#issuecomment-635164520, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGHDDYI2VUYXSVNHTSP3I5DRTYHJDANCNFSM4NMXSSSA.

estebanpw commented 4 years ago

My bad, I updated the repository but forgot to update the release package :-)

First, I assume you were able to generate the .png file of the dotplot and then proceeded to run GECKO with the guide_fastas script to generate the alignments.

NOTE: please update your whole chromeister and gecko repository (I have just pushed an update that improves precision in the alignments from GECKO) and the re-run your experiment completely.

Regarding your question, those coordinates are in the sequence. Also, if you are interested in obtaining the alignments (as text, such as in blast) you can do now by running the "guided_fastas.sh" script with a 1 at the end, in this fashion (remember to update your repos and recompile):

bin/guidefastas.sh X.fasta Y.fasta hits-XY-dotplot.mat.hits 1000 100 60 32 1

The one at the end indicates you want the alignments --beware, if there are many long alignments it will take some time. You can disable this option by running it with a 0 at the end.

Additionally you can visualize the master.csv file here: https://pistacho.ac.uma.es/

Just upload it by using the "Load frags from local" button.

Btw, may I ask the size of your sequences?

Best regards, Esteban

XuewenWangUGA commented 4 years ago

Thanks a lot. It is very helpful.

Xuewen

From: Esteban notifications@github.com Sent: Friday, May 29, 2020 9:49 AM To: estebanpw/chromeister chromeister@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

My bad, I updated the repository but forgot to update the release package :-)

First, I assume you were able to generate the .png file of the dotplot and then proceeded to run GECKO with the guide_fastas script to generate the alignments.

NOTE: please update your whole chromeister and gecko repository (I have just pushed an update that improves precision in the alignments from GECKO) and the re-run your experiment completely.

Regarding your question, those coordinates are in the sequence. Also, if you are interested in obtaining the alignments (as text, such as in blast) you can do now by running the "guided_fastas.sh" script with a 1 at the end, in this fashion:

bin/guidefastas.sh X.fasta Y.fasta hits-XY-dotplot.mat.hits 1000 100 60 32 1

The one at the end indicates you want the alignments --beware, if there are many long alignments it will take some time. You can disable this option by running it with a 0 at the end.

Additionally you can visualize the master.csv file here: https://pistacho.ac.uma.es/

Just upload it by using the "Load frags from local" button.

Btw, may I ask the size of your sequences?

Best regards, Esteban

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/estebanpw/chromeister/issues/3#issuecomment-635982744, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGHDDYK4Y2UWWOWFMZQJQCLRT64QBANCNFSM4NMXSSSA.

XuewenWangUGA commented 4 years ago

In addition, there is another small issue where the removal of "index-refseq-qryseq.csv" is not successful, which cause an error. It seems that that is caused by the directory /path issue.

I already put this information on github so you can fix it.

Xuewen

From: Esteban notifications@github.com Sent: Friday, May 29, 2020 9:49 AM To: estebanpw/chromeister chromeister@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Reopened #3https://github.com/estebanpw/chromeister/issues/3.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/estebanpw/chromeister/issues/3#event-3387268953, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGHDDYK4Y2UWWOWFMZQJQCLRT64QBANCNFSM4NMXSSSA.

XuewenWangUGA commented 4 years ago

Estebanpw,

I have one suggestion. Since the alignment is based on similarity, is that possible to color the dotplot with the similarity score in your scripts?

Xuewen

From: Esteban notifications@github.com Sent: Friday, May 29, 2020 9:49 AM To: estebanpw/chromeister chromeister@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [estebanpw/chromeister] error cannot open file 'dotplot.mat.csv': No such file or directory (#3)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Reopened #3https://github.com/estebanpw/chromeister/issues/3.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/estebanpw/chromeister/issues/3#event-3387268953, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGHDDYK4Y2UWWOWFMZQJQCLRT64QBANCNFSM4NMXSSSA.

estebanpw commented 4 years ago

In the case of the .png dotplot, no, thats not possible due to how chromeister works. However, what you could do is take the .csv that is output by GECKO after using the guide_fastas script, upload here https://pistacho.ac.uma.es/ and then filter by similarity. This will remove alignments that do not meet the similarity threshold. See an example:

imagen

Best regards, Esteban