sebc31/p-gre

P-GRe is a software allowing the prediction of the positions of pseudogenes and their structures on a genome scale.

p-gre's Issues

When using the test data, an error occurred.

#1 (achhhhh) xiajh2@xiajh2:~/data/ach/software/P-GRe$ ./P-GRe_pipeline.sh -f /home/xiajh2/data/ach/software/P-GRe/example/Arabidopsis_thaliana_Chromosome1_partial.fasta -g /home/xiajh2/data/ach/software/P-GRe/example/Arabidopsis_thaliana_Chromosome1_partial.gff
>> Parsing: OK <<
>> Filtering: OK <<
>> Overlaping: OK <<
>> Writing TSV: OK /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/tmp/tblastn_results.tempfile.tsv <<
>> FASTA writing: OK /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/tmp/first_pg_set.tempfile.fasta <<
pg generation:
>> BLAST parsing: OK <<
>> PG generation: 0.00000% <<
pg generation: Error, check: /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/log/PGRe_pseudogene_construct_step.err
#2 The details of the error can be found in the attachment.
PGRe_pseudogene_construct_step.err.txt

I suspect there might be an issue with your gff file, but even after I modified it using tab characters, the error persists. I would appreciate it if you could check both your test data and your code.

error in PGRe_pseudogene_construct_step

Hello,
I'm trying to use P-GRe to detect pseudognenes on Asellidae, but I'm encountering an error. I have no idea how to solve this problem. I did my annotation with Braker3, let me know if you need more detail, I don't know how precise I need to be.

this is the command I used :

./P-GRe_pipeline.sh -f /home/fblanchard/stage_m2/Data/Genome/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.fasta -g /home/fblanchard/stage_m2/Result/Annotation/PKK/braker.gff3 -o /home/fblanchard/stage_m2/Result/P-GRe/PKK/ -t 64 -v

what the programme tells me:

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P-GRe v1.0 starting.
Command:
/home/fblanchard/stage_m2/Tools/P-GRe-main/P-GRe_pipeline.sh -f /home/fblanchard/stage_m2/Data/Genome/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.fasta -g /home/fblanchard/stage_m2/Result/Annotation/PKK/braker.gff3 -o /home/fblanchard/stage_m2/Result/P-GRe/PKK -d /home/fblanchard/stage_m2/Tools/P-GRe-main -t 64 -v

Checking P-GRe installation...
BASNI: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/script/BASNI.py
CConIE: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/script/CConIE.py
PGRe: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/script/PGRe.py
TAGLIA: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/script/TAGLIA.py
VITo: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/script/VITo.py
PolyGet: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/script/PolyGet.py

Checking dependencies...
tblastn: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/bin/tblastn
blastp: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/bin/blastp
makeblastdb: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/bin/makeblastdb
bedtools: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/bin/bedtools
gffread: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/bin/gffread
stretcher: OK /home/fblanchard/stage_m2/Tools/P-GRe-main/bin/stretcher

Checking input files...
FASTA: OK /home/fblanchard/stage_m2/Data/Genome/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.fasta
GFF: OK /home/fblanchard/stage_m2/Result/Annotation/PKK/braker.gff3

Creating working directories and files...
Warning: the requested genome is already in the data/ folder. P-GRe will use the already existing genome.
Warning: the specified GFF file is already in the data/ folder. P-GRe will use the already existing GFF file.
gene-only GFF: OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/braker.gene_only.tempfile.gff
>> INFO: 15381 genes extracted from the GFF file <<
fasta masking: OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna
makeblastdb: OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna
OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna.ndb
OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna.nhr
OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna.nin
OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna.njs
OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna.not
OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna.nsq
OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna.ntf
OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.hard_masked.tempfile.fna.nto
>> INFO: 16354 chromosomes/scaffolds added <<
gffread: OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/Proasellus_karamani_PKK_flye_2023_12_29_asm_flyeHQ.prot.tempfile.faa
>> INFO: 17138 proteins generated <<

---

P-GRe running.

tblastn: OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/proteome_vs_masked_genome_tblastn.blast
filtering hits:
>> Parsing: OK <<
>> Filtering: OK <<
>> Overlaping: OK <<
>> Writing TSV: OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/tblastn_results.tempfile.tsv <<
>> FASTA writing: OK /home/fblanchard/stage_m2/Result/P-GRe/PKK/tmp/first_pg_set.tempfile.fasta <<
pg generation:
>> BLAST parsing: OK <<
>> PG generation: 0.00060% <<
pg generation: Error, check: /home/fblanchard/stage_m2/Result/P-GRe/PKK/log/PGRe_pseudogene_construct_step.err

and the error file :

/opt/src/miniconda3/envs/braker3/lib/python3.9/site-packages/Bio/Application/init.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
warnings.warn(
Traceback (most recent call last):
File "/home/fblanchard/stage_m2/Tools/P-GRe-main/script/PGRe.py", line 280, in
pseudo_prot, pseudogeneDic[pseudogene]['structure_cons'] = TAGLIA.lindleyAlign(alignement,pep_len,error_expected_gap,log)
ValueError: too many values to unpack (expected 2)

Thank you for your help, I remain available.

I also noticed an error during installation: the folder containing the scripts is called scripts with an s, but P-GRe needs it to be called script without an s.

My previous work with the test data proceeded without any issues, but now I encounter errors when using my own data.

          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

Originally posted by @chhhhai in #2 (comment)