Question: Augustus scipio error
0
gravatar for bioinfo17
2.6 years ago by
bioinfo1730
bioinfo1730 wrote:

Hi,

I am trying to use Augustus. However I keep getting the error:

Possibly "scipio" is not installed or not in your PATH at autoAugTrain.pl line 826.

I have seen blat working and scipio.pl running as it has given me a .yaml file. The scipio.err file:

Warning: Query sequences contain gaps and/or premature stopcodons. It will be necessary to remove them if blat is run separately! This is a bug and shouldn't happen. Please report.

Can someone please help?

sequencing • 1.2k views
ADD COMMENTlink modified 23 months ago by mywang20160 • written 2.6 years ago by bioinfo1730
0
gravatar for SES
2.6 years ago by
SES8.1k
Vancouver, BC
SES8.1k wrote:

The script is looking for a program called scipio.pl but can't find it. There is a -scipio option to the script you mention for training Augustus, and you can give that the full path to the scipio program as an argument. The first issue is likely related to the second warning because scipio is actually running blat. No need to speculate about that warning until you run it again with scipio properly configured. If you still have an issue please comment or update your post.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by SES8.1k

Hi SES, when I try executing the autoAugTrain.pl with -scion (full path/scipio.pl) option, it shows:

unknown option:scipio Thanks

ADD REPLYlink written 2.6 years ago by bioinfo1730

Maybe my memory failed me. You'll want to create a link to the script and name the link "scipio.pl" and add the PATH to that directory. The training script is looking for "scipio.pl" specifically.

ADD REPLYlink written 2.6 years ago by SES8.1k

An example would be great - thanks

ADD REPLYlink written 2.6 years ago by bioinfo1730

I did change the path: export PATH=$PATH:/../augustus-3.2.2/scripts/

It runs scipio.pl as it generates a blat.psl file and then a .yaml file. But after that it gets back to the same error:

scipio.pl /augustus-3.2.2/scripts/autoAug/seq/genome_clean.fa ref_transcript.pep > scipio.yaml 2> scipio.err ...Program aborted. Possibly "scipio" is not installed or not in your PATH at /scripts/autoAugTrain.pl line 826. failed to execute: No such file or directory

Since I am a beginner, I don't understand where I am going wrong.

ADD REPLYlink written 2.6 years ago by bioinfo1730
1

You need to add the path to the Scipio directory in the same way. Also, you need to make a link so the program can find "scipio.pl" specifically. For example,

cd /some/path/to/scipio-1.4
ln -s scipio-1.4.1.pl scipio.pl
export PATH=$PATH:`pwd`

should get you past that error.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by SES8.1k

Any updates? Please comment so we can advise further or mark it resolved.

ADD REPLYlink written 2.6 years ago by SES8.1k

I have followed what you have advised. Still the same problem. Generates a .yaml file and then states Program aborted. Possibly "scipio" is not installed or not in your PATH at /augustus-3.2.2/scripts/autoAugTrain.pl line 826.

.err file still shows: Warning: Query sequences contain gaps and/or premature stopcodons. It will be necessary to remove them if blat is run separately! This is a bug and shouldn't happen. Please report.

:(

ADD REPLYlink written 2.6 years ago by bioinfo1730

At the command line, type scipio.pl and show what the output is.

ADD REPLYlink written 2.6 years ago by SES8.1k

Scipio (v1.4) - mapping protein sequences to genomes

usage:
scipio.pl [<options>] <target> <query> 

<target> is a DNA file
<query> is a protein file
both in FASTA format

etc. etc.

ADD REPLYlink written 2.6 years ago by bioinfo1730

I am able to run augustus now, did some modifications (which I shouldn't do) and it's running now. Hasn't crashed yet so far, fingers crossed!!! Thanks for your help.

ADD REPLYlink written 2.6 years ago by bioinfo1730

Okay, good. Please let us know if that solves it. I can add the part about the path to the answer for clarity.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by SES8.1k

I changed the path but it didn't work. So ran scipio outside augustus and used the output files generated to run autoaugtrain.pl and it worked perfect.

ADD REPLYlink written 2.6 years ago by bioinfo1730

can you explain ? I have the issue

ADD REPLYlink written 18 months ago by Picasa390
0
gravatar for mywang2016
23 months ago by
mywang20160
mywang20160 wrote:

Hi, may I ask that how did you deal with the warning "Query sequences contain gaps and/or premature stopcodons. It will be necessary to remove them if blat is run separately!" and make it work successfully?

ADD COMMENTlink written 23 months ago by mywang20160

Hi, I think you just need to keep running it until you finish. I had to ignore the warnings. Even running scipio inside augustus gave me the same warnings.

ADD REPLYlink written 23 months ago by bioinfo1730
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