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sebc31 / P-GRe

P-GRe is a software allowing the prediction of the positions of pseudogenes and their structures on a genome scale.
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My previous work with the test data proceeded without any issues, but now I encounter errors when using my own data. #3

Open chhhhai opened 4 months ago

chhhhai commented 4 months ago 
          I apologize for bothering you again. My previous work with the test data proceeded without any issues, but now I encounter errors when using my own data. Please see the attached file for the details of these errors. If necessary, I can also send you a copy of my data so that you might examine it and identify the root cause of these problems. It is worth mentioning that my GFF3 file was annotated using BRAKER.

PGRe_pseudogene_construct_step.err.txt error

Originally posted by @chhhhai in https://github.com/sebc31/P-GRe/issues/2#issuecomment-2079575598

sebc31 commented 4 months ago 
          I apologize for bothering you again. My previous work with the test data proceeded without any issues, but now I encounter errors when using my own data. Please see the attached file for the details of these errors. If necessary, I can also send you a copy of my data so that you might examine it and identify the root cause of these problems. It is worth mentioning that my GFF3 file was annotated using BRAKER.

PGRe_pseudogene_construct_step.err.txt error

Originally posted by @chhhhai in #2 (comment)

          I apologize for bothering you again. My previous work with the test data proceeded without any issues, but now I encounter errors when using my own data. Please see the attached file for the details of these errors. If necessary, I can also send you a copy of my data so that you might examine it and identify the root cause of these problems. It is worth mentioning that my GFF3 file was annotated using BRAKER.

PGRe_pseudogene_construct_step.err.txt error

Originally posted by @chhhhai in #2 (comment)

Hi ! I apologize for P-GRe not working again. Seems that you have a problem with stretcher binary. Did you follow the instructions concerning stretcher on the home page? I know this one can be tricky to install.

chhhhai commented 4 months ago

This is the command line I used to install stretcher

# EMBOSS:6.6.0.0
wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
tar -xvf EMBOSS-6.6.0.tar.gz
cd EMBOSS-6.6.0
./configure
make
cd ..
cp EMBOSS-6.6.0/emboss/stretcher .
rm EMBOSS-6.6.0.tar.gz

I changed 'cp EMBOSS-6.6.0/emboss/stretcher .' to 'ln -s EMBOSS-6.6.0/emboss/stretcher .', the previous error disappeared, but a new error occurred. The attachment includes my test error file and the new error log file.

ach_test_data.zip PGRe_pseudogene_construct_step.err (2).txt This new issue seems to be related to unpacking

chhhhai commented 4 months ago

When you have a moment, could you please help me with the error you mentioned earlier? I would be extremely grateful. The attachment，includes some test data, has already been sent in my previous comment.