Error in rule asm_gff_stats

[jwli-code]

Hi,
I'm having some problems.
Here is my codes.

cat set_config.sh

daijin configure --scheduler "local" \
     --scoring plant.yaml \
     --copy-scoring plant.yaml \
     -m permissive --sample-sheet sample_sheet.tsv \
     --flank 1000 -i 50 26000 --threads 2 \
     --genome Reference/Bna_ZS11_v0.0.fasta \
     -al hisat -as stringtie -od zs11 --name zs11 \
     -o daijin.yaml --prot-db Reference/total.pep.filter.txt;

daijin assemble -nd --cores 40 daijin.yaml

The following is the error message.

[Tue Jan  9 19:23:35 2024]
Job 34: Computing assembly stats for: zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf
Reason: Missing output files: zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf.stats; Input files updated by another job: zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf

 mikado util stats zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf > zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf.stats
Traceback (most recent call last):
  File "/home/jwli/micromamba/envs/mikado2/bin/mikado", line 11, in <module>
    sys.exit(main())
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/__main__.py", line 18, in main
    from Mikado.subprograms import configure, prepare, serialise, pick, compare, util
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/subprograms/__init__.py", line 6, in <module>
    from . import configure
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/subprograms/configure.py", line 26, in <module>
    from .prepare import parse_prepare_options
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/subprograms/prepare.py", line 22, in <module>
    from ..preparation.prepare import prepare
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/preparation/prepare.py", line 4, in <module>
    from .checking import create_transcript, CheckingProcess
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/preparation/checking.py", line 9, in <module>
    from ..transcripts.transcriptchecker import TranscriptChecker
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/transcripts/__init__.py", line 8, in <module>
    from .transcript import Transcript, Metric
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/transcripts/transcript.py", line 4, in <module>
    from .transcript_methods import splitting, retrieval
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/transcripts/transcript_methods/retrieval.py", line 12, in <module>
    from ...serializers.junction import Junction
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/serializers/__init__.py", line 6, in <module>
    from . import orf
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/serializers/orf.py", line 34, in <module>
    class Orf(DBBASE):
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/Mikado/serializers/orf.py", line 62, in Orf
    query = column_property(select([Query.query_name]).where(
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/sqlalchemy/sql/_selectable_constructors.py", line 489, in select
    return Select(*entities)
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/sqlalchemy/sql/selectable.py", line 5136, in __init__
    self._raw_columns = [
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/sqlalchemy/sql/selectable.py", line 5137, in <listcomp>
    coercions.expect(
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/sqlalchemy/sql/coercions.py", line 413, in expect
    resolved = impl._literal_coercion(
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/sqlalchemy/sql/coercions.py", line 651, in _literal_coercion
    self._raise_for_expected(element, argname)
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/sqlalchemy/sql/coercions.py", line 1137, in _raise_for_expected
    return super()._raise_for_expected(
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/sqlalchemy/sql/coercions.py", line 710, in _raise_for_expected
    super()._raise_for_expected(
  File "/home/jwli/micromamba/envs/mikado2/lib/python3.9/site-packages/sqlalchemy/sql/coercions.py", line 535, in _raise_for_expected
    raise exc.ArgumentError(msg, code=code) from err
sqlalchemy.exc.ArgumentError: Column expression, FROM clause, or other columns clause element expected, got [<sqlalchemy.orm.attributes.InstrumentedAttribute object at 0x7f268fa6bea0>]. Did you mean to say select(<sqlalchemy.orm.attributes.InstrumentedAttribute object at 0x7f268fa6bea0>)?
[Tue Jan  9 19:23:36 2024]
Error in rule asm_gff_stats:
    jobid: 34
    input: zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf
    output: zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf.stats
    shell:
         mikado util stats zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf > zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf.stats
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job asm_gff_stats since they might be corrupted:
zs11/3-assemblies/output/stringtie-0-hisat-SRR6453769-0.gtf.stats
[Tue Jan  9 19:24:17 2024]
Finished job 51.
33 of 56 steps (59%) done
[Tue Jan  9 19:24:31 2024]
Finished job 48.
34 of 56 steps (61%) done
[Tue Jan  9 19:24:46 2024]
Finished job 33.
35 of 56 steps (62%) done
[Tue Jan  9 19:24:53 2024]
Finished job 31.
36 of 56 steps (64%) done
[Tue Jan  9 19:25:30 2024]
Finished job 29.
37 of 56 steps (66%) done
[Tue Jan  9 19:25:36 2024]
Finished job 4.
38 of 56 steps (68%) done
[Tue Jan  9 19:25:59 2024]
Finished job 42.
39 of 56 steps (70%) done
[Tue Jan  9 19:27:57 2024]
Finished job 45.
40 of 56 steps (71%) done
[Tue Jan  9 19:28:46 2024]
Finished job 39.
41 of 56 steps (73%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-01-09T181733.051352.snakemake.log