Augustus scipio error

Question

[bioinfo17]

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?

Answer 1

[SES]

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.

[bioinfo17]

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

unknown option:scipio Thanks

[SES]

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.

[bioinfo17]

An example would be great - thanks

[bioinfo17]

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.

[SES]

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.

[SES]

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

[bioinfo17]

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.

:(

[SES]

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

[bioinfo17]

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.

[bioinfo17]

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.

[SES]

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

[bioinfo17]

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.

[Picasa]

can you explain ? I have the issue

Answer 2

[mywang2016]

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?

[bioinfo17]

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.