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Gaius-Augustus / GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.
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pygustus error #10

Closed CongLiu37 closed 1 year ago

CongLiu37 commented 1 year ago

Hello,

I encountered following error with pyaugustus when running test1:

# Thu Mar  2 11:27:42 2023: Log information is stored in file /home/c/c-liu/Softwares/GALBA/example/tests/test1/GALBA.log
[M::mp_idx_restore@0.597*0.13] loaded the index
[M::mp_idx_print_stat] 280767 distinct k-mers; mean occ of infrequent k-mers: 1.52; 0 frequent k-mers accounting for 0 occurrences
[M::worker_pipeline::0.779*0.85] mapped 259 sequences
[M::main] Version: 0.7-r216-dirty
[M::main] CMD: /home/c/c-liu/Softwares/miniprot//miniprot -ut8 --gtf /home/c/c-liu/Softwares/GALBA/example/tests/test1/genome.mpi /home/c/c-liu/Softwares/GALBA/example/tests/../proteins.fa
[M::main] Real time: 0.783 sec; CPU: 0.667 sec; Peak RSS: 0.070 GB
#*********
# WARNING: Number of reliable training genes is low (226). Recommended are at least 600 genes
#*********
ERROR in file /home/c/c-liu/Softwares/GALBA/scripts/galba.pl at line 4895
Failed to execute: /home/c/c-liu/miniconda3/bin//python3 /home/c/c-liu/Softwares/GALBA/example/tests/test1/pygustus_hints.py 1> /home/c/c-liu/Softwares/GALBA/example/tests/test1/pygustus_hints.out 2>/home/c/c-liu/Softwares/GALBA/example/tests/test1/errors/pygustus_hints.err

real    0m23.895s
user    0m15.373s
sys 0m3.113s

and here is the error message for pyaugustus_hints.py:

Traceback (most recent call last):
  File "/home/c/c-liu/Softwares/GALBA/example/tests/test1/pygustus_hints.py", line 9, in <module>
    augustus.predict('/home/c/c-liu/Softwares/GALBA/example/tests/test1/genome.fa', species='Sp_1', partitionLargeSequences=True, partitionHints=True, minSplitSize=1000000, chunksize=2500000, jobs=8, **augargs)
  File "/home/c/c-liu/miniconda3/lib/python3.9/site-packages/pygustus/augustus.py", line 42, in predict
    pygustus_options = util.get_options(
  File "/home/c/c-liu/miniconda3/lib/python3.9/site-packages/pygustus/util.py", line 115, in get_options
    options = AugustusOptions(
  File "/home/c/c-liu/miniconda3/lib/python3.9/site-packages/pygustus/options/aug_options.py", line 87, in __init__
    self.set_value(option, value)
  File "/home/c/c-liu/miniconda3/lib/python3.9/site-packages/pygustus/options/aug_options.py", line 101, in set_value
    raise ValueError(
ValueError: Invalid Parameter for Augustus: partitionLargeSequences

Sincerely,

Cong

KatharinaHoff commented 1 year ago

Are you using the container? Are you using the latest container version?

If not, please update the container/use the container.

If you are running outside the container, you have to update your Augustus to the latest code in the master branch on Github. There is a typo in a json file that causes the problem.

Cong Liu @.***> schrieb am Do. 2. März 2023 um 03:35:

Hello,

I encountered following error with pyaugustus when running test1:

Thu Mar 2 11:27:42 2023: Log information is stored in file /home/c/c-liu/Softwares/GALBA/example/tests/test1/GALBA.log

@.***0.13] loaded the index [M::mp_idx_print_stat] 280767 distinct k-mers; mean occ of infrequent k-mers: 1.52; 0 frequent k-mers accounting for 0 occurrences [M::worker_pipeline::0.7790.85] mapped 259 sequences [M::main] Version: 0.7-r216-dirty [M::main] CMD: /home/c/c-liu/Softwares/miniprot//miniprot -ut8 --gtf /home/c/c-liu/Softwares/GALBA/example/tests/test1/genome.mpi /home/c/c-liu/Softwares/GALBA/example/tests/../proteins.fa [M::main] Real time: 0.783 sec; CPU: 0.667 sec; Peak RSS: 0.070 GB

*****

WARNING: Number of reliable training genes is low (226). Recommended are at least 600 genes

*****

ERROR in file /home/c/c-liu/Softwares/GALBA/scripts/galba.pl at line 4895 Failed to execute: /home/c/c-liu/miniconda3/bin//python3 /home/c/c-liu/Softwares/GALBA/example/tests/test1/pygustus_hints.py 1> /home/c/c-liu/Softwares/GALBA/example/tests/test1/pygustus_hints.out 2>/home/c/c-liu/Softwares/GALBA/example/tests/test1/errors/pygustus_hints.err

real 0m23.895s user 0m15.373s sys 0m3.113s

and here is the error message for pyaugustus_hints.py:

Traceback (most recent call last): File "/home/c/c-liu/Softwares/GALBA/example/tests/test1/pygustus_hints.py", line 9, in augustus.predict('/home/c/c-liu/Softwares/GALBA/example/tests/test1/genome.fa', species='Sp_1', partitionLargeSequences=True, partitionHints=True, minSplitSize=1000000, chunksize=2500000, jobs=8, **augargs) File "/home/c/c-liu/miniconda3/lib/python3.9/site-packages/pygustus/augustus.py", line 42, in predict pygustus_options = util.get_options( File "/home/c/c-liu/miniconda3/lib/python3.9/site-packages/pygustus/util.py", line 115, in get_options options = AugustusOptions( File "/home/c/c-liu/miniconda3/lib/python3.9/site-packages/pygustus/options/aug_options.py", line 87, in init self.set_value(option, value) File "/home/c/c-liu/miniconda3/lib/python3.9/site-packages/pygustus/options/aug_options.py", line 101, in set_value raise ValueError( ValueError: Invalid Parameter for Augustus: partitionLargeSequences

Sincerely,

Cong

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CongLiu37 commented 1 year ago

Works now. Thank you!