fix nucleotides option on MWAS

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fix nucleotides option on MWAS

Humann, Jodi Lynn

Hello,

 

I was wondering if there was any way to enable the ‘–fix_nucleotides’ option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

 

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

 

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

 

Thanks,

Jodi

 

Jodi Humann, Ph.D.

Main Bioinformatics Lab Project Coordinator

Department of Horticulture

Washington State University

PO Box 646414

Pullman, WA 99164-6414

509-335-3206

[hidden email]

 

 


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Re: fix nucleotides option on MWAS

Carson Holt-2
Hi Jodi,

I didn’t even know anyone else even had an MWAS server running (I’ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (…/maker/MWAS/bin/mwas_server).

Somewhere inside the script there will be a line like this —>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It’s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N’s.

Thanks,
Carson


On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <[hidden email]> wrote:

Hello,
 
I was wondering if there was any way to enable the ‘–fix_nucleotides’ option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
 
ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
 
The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
 
Thanks,
Jodi
 
Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
 
 
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Re: fix nucleotides option on MWAS

Humann, Jodi Lynn

Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?

 

Jodi

 

From: Carson Holt [mailto:[hidden email]]
Sent: Thursday, October 19, 2017 10:33 AM
To: Humann, Jodi Lynn <[hidden email]>
Cc: [hidden email]
Subject: Re: [maker-devel] fix nucleotides option on MWAS

 

Hi Jodi,

 

I didn’t even know anyone else even had an MWAS server running (I’ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (…/maker/MWAS/bin/mwas_server).

 

Somewhere inside the script there will be a line like this —>

 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";

 

You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It’s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N’s.

 

Thanks,

Carson

 

 

On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <[hidden email]> wrote:

 

Hello,

 

I was wondering if there was any way to enable the ‘–fix_nucleotides’ option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:

 

ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2

 

The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.

 

Thanks,

Jodi

 

Jodi Humann, Ph.D.

Main Bioinformatics Lab Project Coordinator

Department of Horticulture

Washington State University

PO Box 646414

Pullman, WA 99164-6414

509-335-3206

 

 

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Re: fix nucleotides option on MWAS

Carson Holt-2
Yes. That is the current version.

—Carson

On Oct 19, 2017, at 12:45 PM, Humann, Jodi Lynn <[hidden email]> wrote:

Thanks for the info, Carson.  We are running v2.31.9, and were able to get MWAS running, with some work.  That is the current Maker version right?
 
Jodi
 
From: Carson Holt [[hidden email]] 
Sent: Thursday, October 19, 2017 10:33 AM
To: Humann, Jodi Lynn <[hidden email]>
Cc: [hidden email]
Subject: Re: [maker-devel] fix nucleotides option on MWAS
 
Hi Jodi,
 
I didn’t even know anyone else even had an MWAS server running (I’ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing the mwas_server script (…/maker/MWAS/bin/mwas_server).
 
Somewhere inside the script there will be a line like this —>
 $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";
 
You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It’s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N’s.
 
Thanks,
Carson
 
 
On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <[hidden email]> wrote:
 
Hello,
 
I was wondering if there was any way to enable the ‘–fix_nucleotides’ option on the MWAS version we are running locally on our server?  I have a genome sequence with a degenerate nucleotide and get the following error:
 
ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2
 
The error message says the option can be used on the command line.  Is that set on the actual command to run Maker (when using the command line version), or is it something that can be set in one of the control files?  Any input would be greatly appreciated.  I know I can fix my input file, but would prefer to just enable the option if I can.
 
Thanks,
Jodi
 
Jodi Humann, Ph.D.
Main Bioinformatics Lab Project Coordinator
Department of Horticulture
Washington State University
PO Box 646414
Pullman, WA 99164-6414
509-335-3206
 
 
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org