errors-optimize_augustus.stderr

[enriquepola1996]

Hello,

I am running Braker3 using only proteins but I am stuck on this part, could you help me? I installed Braker3 with singularity as indicated on the page.

My command:

 singularity exec braker3.sif braker.pl --genome=fungal_mask.fasta --prot_seq=Fungi.fa --gff3 --threads 8

# Wed May  1 22:52:25 2024: Computing accuracy of AUGUSTUS prediction (in test file derived from predictions on training data set stored in /home/braker3/braker/firsttest.stdout)
# Wed May  1 22:52:25 2024: The accuracy after initial training (no optimize_augustus.pl, no CRF) is 0.871066666666667
# Wed May  1 22:52:25 2024: optimizing AUGUSTUS parameters
/usr/bin/perl /opt/Augustus/scripts/optimize_augustus.pl --aug_exec_dir=/opt/Augustus/bin/ --rounds=5 --species=Sp_2 --kfold=8 --AUGUSTUS_CONFIG_PATH=/home/.augustus --onlytrain=/home/braker3/braker/train.gb.train.train --cpus=8 /home/braker3/braker/train.gb.train.test 1>/home/braker3/braker/optimize_augustus.stdout 2>/home/braker3/braker/errors/optimize_augustus.stderr

[KatharinaHoff]

What is the content of the stdout and stderr files?

On Thu, May 2, 2024 at 7:17 AM enriquepola1996 @.***> wrote:

Hello,

I am running Braker3 using only proteins but I am stuck on this part, could you help me? I installed Braker3 with singularity as indicated on the page.

Wed May 1 22:52:25 2024: Computing accuracy of AUGUSTUS prediction (in test file derived from predictions on training data set stored in /home/braker3/braker/firsttest.stdout)

Wed May 1 22:52:25 2024: The accuracy after initial training (no optimize_augustus.pl, no CRF) is 0.871066666666667

Wed May 1 22:52:25 2024: optimizing AUGUSTUS parameters

/usr/bin/perl /opt/Augustus/scripts/optimize_augustus.pl --aug_exec_dir=/opt/Augustus/bin/ --rounds=5 --species=Sp_2 --kfold=8 --AUGUSTUS_CONFIG_PATH=/home/.augustus --onlytrain=/home/braker3/braker/train.gb.train.train --cpus=8 /home/braker3/braker/train.gb.train.test 1>/home/braker3/braker/optimize_augustus.stdout 2>/home/braker3/braker/errors/optimize_augustus.stderr

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[enriquepola1996]

Hello, thanks for the answer,

Are you referring to this?

(base) user@DESKTOP-62E8R2K:~/braker3/braker/errors$ ls
GeneMark-EP.stderr                  etrainFilterGenes.stderr       find_python3_re.err       new_species.stderr
GeneMark-ES.stderr                  filterGenemark.stderr          firstetraining.stderr     optimize_augustus.stderr
aa2nonred.stderr                    filterGenesIn.stderr           firsttest.stderr          randomSplit.stderr
downsample_traingenes.err           filterGenesIn_mRNAname.stderr  gbFilterEtraining.stderr  sortGeneMark.err
ensure_min_n_training_genes.stderr  find_python3_biopython.err     gc_content.stderr         traingenes.gtf_gff2gbSmallDNA.stderr

[KatharinaHoff]

No, I am referring to the two output files the last command that braker executed. There are two files names with full paths given.

On Thu, May 2, 2024 at 7:38 AM enriquepola1996 @.***> wrote:

Hello, thanks for the answer,

Are you referring to this?

(base) @.***:~/braker3/braker/errors$ ls GeneMark-EP.stderr etrainFilterGenes.stderr find_python3_re.err new_species.stderr GeneMark-ES.stderr filterGenemark.stderr firstetraining.stderr optimize_augustus.stderr aa2nonred.stderr filterGenesIn.stderr firsttest.stderr randomSplit.stderr downsample_traingenes.err filterGenesIn_mRNAname.stderr gbFilterEtraining.stderr sortGeneMark.err ensure_min_n_training_genes.stderr find_python3_biopython.err gc_content.stderr traingenes.gtf_gff2gbSmallDNA.stderr

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[KatharinaHoff]

Do you mean "is running a long time" with being stuck, or do you mean it actually died? If it is just running, keep it running. This can take several days with 8 threads, depending on the training gene properties.

On Thu, May 2, 2024 at 7:41 AM Katharina Hoff @.***> wrote:

No, I am referring to the two output files the last command that braker executed. There are two files names with full paths given.

On Thu, May 2, 2024 at 7:38 AM enriquepola1996 @.***> wrote:

Hello, thanks for the answer,

Are you referring to this?

(base) @.***:~/braker3/braker/errors$ ls GeneMark-EP.stderr etrainFilterGenes.stderr find_python3_re.err new_species.stderr GeneMark-ES.stderr filterGenemark.stderr firstetraining.stderr optimize_augustus.stderr aa2nonred.stderr filterGenesIn.stderr firsttest.stderr randomSplit.stderr downsample_traingenes.err filterGenesIn_mRNAname.stderr gbFilterEtraining.stderr sortGeneMark.err ensure_min_n_training_genes.stderr find_python3_biopython.err gc_content.stderr traingenes.gtf_gff2gbSmallDNA.stderr

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[enriquepola1996]

Thanks,

firsttest.stdout:

# Read in 4354 genbank sequences.
Quantiles of the GC contents in the training set:
0%  0.348
5%  0.435   10% 0.447
15% 0.456   20% 0.464
25% 0.471   30% 0.476
35% 0.481   40% 0.485
45% 0.49    50% 0.494
55% 0.498   60% 0.502
65% 0.506   70% 0.51
75% 0.515   80% 0.519
85% 0.525   90% 0.532
95% 0.541   100%    0.602
HMM-training the parameters...
i= 0 bc= (0.237, 0.263, 0.263, 0.237)
 ** building model for exons *EXON*
start codon frequencies: ATG(4354)
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
 number of bases in the reading frames: 2315733 2320074 2320075
--- frame = 0 ---    minPatSum = 233
--- frame = 1 ---    minPatSum = 233
--- frame = 2 ---    minPatSum = 233
--- initial frame = 0 ---    minPatSum = 233
--- initial frame = 1 ---    minPatSum = 233
--- initial frame = 2 ---    minPatSum = 233
--- internal exon terminal frame = 0 ---    minPatSum = 233
--- internal exon terminal frame = 1 ---    minPatSum = 233
--- internal exon terminal frame = 2 ---    minPatSum = 233
single, initial, internal, terminal mean exon lengths :
1020    285 331 543
single exon : 287
initial exon 0 : 1663
initial exon 1 : 1377
initial exon 2 : 1027
internal exon 0 : 2774
internal exon 1 : 2294
internal exon 2 : 1948
terminal exon : 4067
Frequency of stop codons:
tag: 1128 (0.259)
taa: 1902 (0.437)
tga: 1324 (0.304)
end *EXON*
Storing parameters to file...
Writing exon model parameters [1] to file /home/enriquepola/.augustus/species/Sp_2/Sp_2_exon_probs.pbl.

optimize_augustus.stderr: Is empty

[enriquepola1996]

On my server I have also had problems with something similar::

[Tue Apr 30 19:19:39 2024] Alignment of pairs finished
[Tue Apr 30 19:19:39 2024] Translating coordinates from local pair level to contig level
[Tue Apr 30 19:19:55 2024] Finished spliced alignment
[Tue Apr 30 19:19:55 2024] Flagging top chains
[Tue Apr 30 19:20:12 2024] Processing the output
[Tue Apr 30 19:20:56 2024] Output processed
[Tue Apr 30 19:20:56 2024] ProtHint finished.
ERROR in file /data/software/BRAKER3/BRAKER-3.0.8/scripts/braker.pl at line 6288
Failed to execute: /data/software/Augustus-3.5.0/bin/etraining --species=Trichoderma_harzianum_T6 --AUGUSTUS_CONFIG_PATH=/usuario/epola/braker/augustus_config /NFS/usuario/BRAKER3_abril/BRAKER_enrique_T6/braker/train.f.gb 1> /NFS/usuario/BRAKER3_abril/BRAKER_enrique_T6/braker/gbFilterEtraining.stdout 2>/NFS/usuario/BRAKER3_abril/BRAKER_enrique_T6/braker/errors/gbFilterEtraining.stderr

gbFilterEtraining.stderr: Is empty

[enriquepola1996]

No, this process has not died, it has just been there for a while, I thought it would be a little faster since it is a very small fungal genome, I will continue waiting. On the other hand, the process on my server has died.