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bichangwei / PMAT

An efficient assembly tool for plant mitochondrial genome
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Can't use v1.2.2 #20

Open tallnuttrbgv opened 6 months ago

tallnuttrbgv commented 6 months ago

Hi,

I need to use v1.2.2 because I cannot install apptainer. However, this version prints a vast amount of messages to STDOUT, exceeding limits.

Thanks.

yunmika commented 5 months ago

The latest version has modified the log output problem, if you choose the old version you can choose to output directly to the console. Please let me know if you have any other questions.

Hi,

I need to use v1.2.2 because I cannot install apptainer. However, this version prints a vast amount of messages to STDOUT, exceeding limits.

Thanks.

tallnuttrbgv commented 5 months ago

I can't install apptainer, so can't use latest version.

1.2.2 is giving this error:

Error: An internal error has occurred in the computation. Assertion: canModify(chord->getId()) Location: 'bool ChordMatrix::checkAddChordColumn(Chord*, int)' [ChordMatrix.cpp:224] Please report this error to your customer support representative. Reads assembly end. >>> 2024-04-10 19:47:39 [ WARNING 2024-04-10 19:47:39 ] Data assembly error: Please change the -fc or -sd option.

tallnuttrbgv commented 5 months ago

I fixed the stdout problem by commenting the print command in run_assembler.py, but get the error above.

yunmika commented 5 months ago

I fixed the stdout problem by commenting the print command in run_assembler.py, but get the error above.

We prefer to install the VM and download the apptainer so that you can use the latest version and avoid such problems. Of course we will rework the old version later, which may take a while.