BinSpreader Error

[pbelmann]

Description of bug

In version 4.3.0, executing binSpreader on Linux returns a stack trace, even without providing parameters.

SYNOPSIS
        binspreader <graph (in binary or GFA)> <file with binning from binner in .tsv format>
                    <output path to write binning results after propagation> [--paths
                    <contig.paths>] [--dataset <yaml>] [-l <value>] [-t <value>] [-e <eps>] [-n
                    <value>] [-m] [-Smax|-Smle] [-Rcorr|-Rprop] [--cami] [--zero-bin] [--tall-multi]
                    [--bin-dist] [-la <labeled alpha>] [--sparse-propagation] [--no-unbinned-bin]
                    [-ma <--metaalpha>] [-lt <--length-threshold>] [-db <--distance-bound>] [-r] [-b
                    <threshold>] [--bin-load] [--debug] [--tmp-dir <dir>]

OPTIONS
        --paths <contig.paths>
                    use contig paths from file

        --dataset <yaml>
                    dataset description (in YAML)

        -l <value>  library index (0-based, default: 0)
        -t <value>  # of threads to use
        -e <eps>    convergence relative tolerance threshold
        -n <value>  maximum number of iterations
        -m          allow multiple bin assignment
        -Smax|-Smle binning assignment strategy
        -Rcorr|-Rprop
                    binning refiner type

        --cami      use CAMI bioboxes binning format
        --zero-bin  emit zero bin for unbinned sequences
        --tall-multi
                    use tall table for multiple binning result

        --bin-dist  estimate pairwise bin distance (could be slow on large graphs!)
        -la <labeled alpha>
                    labels correction alpha for labeled data

        Sparse propagation options:
            --sparse-propagation
                    Gradually reduce alpha from binned to unbinned edges

            --no-unbinned-bin
                    Do not create a special bin for unbinned contigs

            -ma <--metaalpha>
                    Labels correction alpha for sparse propagation procedure

            -lt <--length-threshold>
                    Binning will not be propagated to edges longer than threshold

            -db <--distance-bound>
                    Binning will not be propagated further than bound

        Read splitting options:
            -r, --reads
                    split reads according to binning

            -b, --bin-weight <threshold>
                    reads bin weight threshold

        Developer options:
            --bin-load
                    load binary-converted reads from tmpdir

            --debug produce lots of debug data
            --tmp-dir <dir>
                    scratch directory to use
WARNING: Try to use logger before create one. Level=ERROR. Message=Invalid command line arguments
=== Stack Trace ===
./bin/binspreader() [0x443759]
./bin/binspreader() [0x4411c4]
./bin/binspreader() [0x429aee]
/lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca) [0x7282a842a1ca]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b) [0x7282a842a28b]
./bin/binspreader() [0x430c3e]

spades.log

I have not seen a log file. It doesn't seem to have been created.

params.txt

Have not used a param file

SPAdes version

4.3.0

Operating System

Ubuntu 24.04.4 LTS

Python Version

3.12.3

Method of SPAdes installation

binaries

No errors reported in spades.log

• Yes