Error in transferring annotations to a new assembly using RATT

Question

[Jautis]

Hello, I am using RATT to try and transfer gene annotations from a published genome to a new assembly for a sister taxa. However, I am getting an error message (copied below). Following this message, RATT finishes running, but fails to transfer any of the annotations. This error message remains after double-checking all relevant paths and reinstalling RATT. Any idea what could be going wrong?

I've included code here which replicates this error (for me) using the example dataset available at http://ratt.sourceforge.net/example.html. Thank you in advance for your help!

My code:

##Get PAGIT, which now wraps RATT. https://www.sanger.ac.uk/science/tools/pagit
cd ~/Programs/; wget ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.64bit.tgz
tar xzf PAGIT.V1.64bit.tgz; ./installme.sh
## set up path and links to run RATT
#PATH=$PATH:~/Programs/MUMmer3.23/, I don't think this is necessary -- nucmer is included withing PAGIT
PAGIT_HOME=~/Programs/PAGIT
RATT_HOME=$PAGIT_HOME/RATT/; export RATT_HOME
RATT_CONFIG=$RATT_HOME/RATT.config_euk; export RATT_CONFIG
PATH=$PATH:$PAGIT_HOME; PATH=$PATH:$PAGIT_HOME/bin

##Get the example dataset
cd ~/data; wget http://ratt.sourceforge.net/Tbexample.zip; unzip Tbexample.zip
mkdir embl; mv Tb_H37Rv.embl embl
##Attempt to run RATT
##note: replaced "SimStrain" with "Strain" because "SimStrain" is not a supported transfer type
$RATT_HOME/start.ratt.sh embl F11.fasta F11 Strain

Error output:

ERROR: Could not parse delta file, nucmer.F11.delta
error no: 400
ERROR: Could not parse delta file, nucmer.F11.filter.delta
error no: 402
ERROR: Could not parse delta file, nucmer.F11.delta
error no: 400
ERROR: Could not parse delta file, nucmer.F11.filter.delta
error no: 402
Use of uninitialized value $stats in print at /data/tunglab/tpv/Programs/RATT//main.ratt.pl line 94.

[cschu181]

Don't you need to export PATH after modifying it?

Another thing: have you tried the standalone version of RATT? That one works for me with the example.

Last: I don't see any sign for this in your output, but the RATT code uses a deprecated feature that is not compatible with more modern Perl installations. I have contacted the author about this, but he's not back from the holidays yet.

[Jautis]

Thank you for the response! Thank you for noting I should export the PATH, but that doesn't resolve the problem.

By standalone version, do you mean the one from https://svn.code.sf.net/p/ratt/code/? I just tried that, but it returned the same error message.

It sounds like you've been able to make RATT work around this deprecated feature, what would I need to change? I don't know the underlying code well enough to know if this is consistent with the error I'm seeing

[cschu181]

1) Ok, was worth a try. 2) Yes, I meant that version. Since that doesn't work I'll agree with Lieven Sterck about the potential nucmer issue. 3) This is probably not related to your issue, but this is what you have to change in main.ratt.pl:

229c229
<     if (defined(@{$$ref_shift{$refName}})) {
---
>     if (@{$$ref_shift{$refName}}) {

edit: more comprehensive answer

[anisha.zaveri]

Using the standalone version solved this for me. Thanks!

[lieven.sterck]

might be an incompatibility issue with nucmer, think I've seen this before. Which version of MUMmer do they recommend using?

[Jautis]

This seems likely, but they don't recommend a version to use. There's also a copy of nucmer within PAGIT I can refer to, but that doesn't change anything either

[lieven.sterck]

perhaps you can find some inspiration here ? something like specifically pointing them to specified directory

[cschu181]

I am using mummer-4.0.0beta2/mummer3.23 (the latter one installed with conda) and it works for me. Maybe include the commented out mummer-addition to the path and export the path to see how that goes. Just because PAGIT brings its own mummer it doesn't necessarily add it to the path (although I might be wrong here).

edit: more detail