Error running sinefinder

[soungalo]

I am running reasonaTE with the sinefind tool on a 30Mb sequence and getting the error message:

maximum recursion depth exceeded while calling a Python object
sine_finder_version=1.0.1

ERROR 00: unrecognized error
maximum recursion depth exceeded while calling a Python object
sine_finder_version=1.0.1

ERROR 00: unrecognized error

Has anyone encountered this before? Any way to fix this or should I just give up on sinefinder?

[DerKevinRiehl]

Hello Lior Glick, thank you for your interest in reasonaTE and transposonUltimate.

Could you please share the full console output (inclusive your statement to run)?

From what you shared, it is hard to assess the issue.

Thank you, Best regards, Kevin

[soungalo]

The command I ran was:

conda activate transposon_annotation_tools_env
export PATH=$CONDA_PREFIX/bin:$PATH
reasonaTE -mode annotate -projectFolder <projectName> -projectName <projectName> -tool sinefind > sinefind.out 2> sinefind.err

sinefind.out:

{'OVERLAP': 8000, 'OUTTYPE': 'fasta', 'TSD_MIN_WORDSIZE': 5, 'verbose': 1, 'TSD_MISMATCH_TOLERANCE': 2, 'RUNTYPE': 'seqwise', 'TSD_SCORE_CUTOFF': 10, 'TSD_ORIENTATION': 'F', 'TSD_MISMATCH_PENALTY': 1, 'CHUNKSIZE': 100000}
Run started: 2023-03-15 10:24:14

   processing (0) 'seq1', segment 0:30427671 SEQLEN= 30427671
   searching forward
{'OVERLAP': 8000, 'OUTTYPE': 'fasta', 'TSD_MIN_WORDSIZE': 5, 'verbose': 1, 'TSD_MISMATCH_TOLERANCE': 2, 'RUNTYPE': 'seqwise', 'TSD_SCORE_CUTOFF': 10, 'TSD_ORIENTATION': 'F', 'TSD_MISMATCH_PENALTY': 1, 'CHUNKSIZE': 100000}
Run started: 2023-03-15 10:52:31

   processing (0) 'seq1', segment 0:30427671 SEQLEN= 30427671
   searching forward
Annotation by software  sinefind  finished successfully...

sinefind.err:

maximum recursion depth exceeded while calling a Python object
sine_finder_version=1.0.1

ERROR 00: unrecognized error
maximum recursion depth exceeded while calling a Python object
sine_finder_version=1.0.1

ERROR 00: unrecognized error

[DerKevinRiehl]

Hello Lior Glick, fromt he outputs it seems that the tool sine_finder itself has a problem with your given project / data. As we were just packaging the existing software into conda packages but did not develop them, it will hard to help you with this one.

However, I think you can just skip this software in your pipeline and continue with the many other tools? A verification that your FASTA file is okay with other tools might be a good suggestion.

Hope I could help`? Best, Kevin