pygustus error

[CongLiu37]

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]

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::0.779*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 — Reply to this email directly, view it on GitHub <#10>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJMC6JHNPZGHU3HQAEPGADTW2ABQFANCNFSM6AAAAAAVMZXVYI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[CongLiu37]

Works now. Thank you!