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bioconvert / bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
http://bioconvert.readthedocs.io
GNU General Public License v3.0
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got many warnings when call bioconvert --help #256

Closed lufuhao closed 2 years ago

lufuhao commented 3 years ago

For bug reporting, please fill the form here below and set the label to "bug" in the right hand side. Otherwise, just remove this content and fill your issue as normal.

Platform

ubuntu 20.04 gcc 9.3 python3.8 pip3 20.0.2

Version of bioconvert

v0.4.3 from pypi

Command or code used

bioconvert fastq2fasta --help

Expected behaviour

10 lines

Your results

site-packages/bioconvert/core/benchmark.py:27: FutureWarning: The pandas.np module is deprecated and will be removed from pandas in a future version. Import numpy directly instead from pandas import np

WARNING [bioconvert.core.base:152]: converter 'BAM2BEDGRAPH': method mosdepth is not available WARNING [bioconvert.core.base:152]: converter 'BAM2BIGWIG': method bamCoverage is not available WARNING [bioconvert.core.base:152]: converter 'BAM2COV': method samtools is not available WARNING [bioconvert.core.base:152]: converter 'BAM2CRAM': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'BAM2CRAM' for ('bam',) -> ('cram',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BAM2FASTA': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'BAM2FASTA' for ('bam',) -> ('fasta',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2FASTA' for ('bam',) -> ('fa',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2FASTA' for ('bam',) -> ('fst',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BAM2FASTQ': method samtools is not available WARNING [bioconvert.core.base:152]: converter 'BAM2JSON': method bamtools is not available WARNING [bioconvert.core.registry:117]: converter 'BAM2JSON' for ('bam',) -> ('json',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BAM2SAM': method pysam is not available WARNING [bioconvert.core.base:152]: converter 'BAM2SAM': method sambamba is not available WARNING [bioconvert.core.base:152]: converter 'BAM2SAM': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'BAM2SAM' for ('bam',) -> ('sam',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BAM2TSV': method pysam is not available WARNING [bioconvert.core.base:152]: converter 'BAM2TSV': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'BAM2TSV' for ('bam',) -> ('tsv',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BAM2WIGGLE': method wiggletools is not available WARNING [bioconvert.core.registry:117]: converter 'BAM2WIGGLE' for ('bam',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2WIGGLE' for ('bam',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BCF2VCF': method bcftools is not available WARNING [bioconvert.core.registry:117]: converter 'BCF2VCF' for ('bcf',) -> ('vcf',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BCF2WIGGLE': method wiggletools is not available WARNING [bioconvert.core.registry:117]: converter 'BCF2WIGGLE' for ('bcf',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BCF2WIGGLE' for ('bcf',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BED2WIGGLE': method wiggletools is not available WARNING [bioconvert.core.registry:117]: converter 'BED2WIGGLE' for ('bed',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BED2WIGGLE' for ('bed',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BEDGRAPH2WIGGLE': method wiggletools is not available WARNING [bioconvert.core.registry:117]: converter 'BEDGRAPH2WIGGLE' for ('bedgraph',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BEDGRAPH2WIGGLE' for ('bedgraph',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BEDGRAPH2WIGGLE' for ('bg',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BEDGRAPH2WIGGLE' for ('bg',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BIGBED2WIGGLE': method wiggletools is not available WARNING [bioconvert.core.registry:117]: converter 'BIGBED2WIGGLE' for ('bb',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGBED2WIGGLE' for ('bb',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGBED2WIGGLE' for ('bigbed',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGBED2WIGGLE' for ('bigbed',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BIGWIG2WIGGLE': method wiggletools is not available WARNING [bioconvert.core.registry:117]: converter 'BIGWIG2WIGGLE' for ('bigwig',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGWIG2WIGGLE' for ('bigwig',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGWIG2WIGGLE' for ('bw',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGWIG2WIGGLE' for ('bw',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BPLINK2PLINK': method plink is not available WARNING [bioconvert.core.registry:117]: converter 'BPLINK2PLINK' for ('bplink',) -> ('plink',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'BPLINK2VCF': method plink is not available WARNING [bioconvert.core.registry:117]: converter 'BPLINK2VCF' for ('bplink',) -> ('vcf',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'CLUSTAL2FASTA': method goalign is not available WARNING [bioconvert.core.base:152]: converter 'CLUSTAL2FASTA': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'CLUSTAL2NEXUS': method goalign is not available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clustal',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clustal',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clustal',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clustal',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('aln',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('aln',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('aln',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('aln',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clw',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clw',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clw',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clw',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'CLUSTAL2PHYLIP': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'CLUSTAL2STOCKHOLM': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'CRAM2BAM': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'CRAM2BAM' for ('cram',) -> ('bam',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'CRAM2FASTA': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTA' for ('cram',) -> ('fasta',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTA' for ('cram',) -> ('fa',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTA' for ('cram',) -> ('fst',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'CRAM2FASTQ': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTQ' for ('cram',) -> ('fastq',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTQ' for ('cram',) -> ('fq',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'CRAM2SAM': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'CRAM2SAM' for ('cram',) -> ('sam',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'DSRC2GZ': method dsrcpigz is not available WARNING [bioconvert.core.registry:117]: converter 'DSRC2GZ' for ('dsrc',) -> ('gz',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'EMBL2FASTA': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'EMBL2GENBANK': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'FASTA2CLUSTAL': method goalign is not available WARNING [bioconvert.core.base:152]: converter 'FASTA2CLUSTAL': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'FASTA2GENBANK': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'FASTA2NEXUS': method goalign is not available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fasta',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fasta',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fasta',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fasta',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fa',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fa',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fa',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fa',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fst',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fst',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fst',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fst',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'FASTA2PHYLIP': method goalign is not available WARNING [bioconvert.core.base:152]: converter 'FASTA2PHYLIP': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'GENBANK2EMBL': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'GENBANK2FASTA': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'GZ2BZ2': method pigz_pbzip2 is not available WARNING [bioconvert.core.base:152]: converter 'GZ2DSRC': method pigzdsrc is not available WARNING [bioconvert.core.registry:117]: converter 'GZ2DSRC' for ('gz',) -> ('dsrc',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'NEWICK2NEXUS': method gotree is not available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('newick',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('newick',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('newick',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('newick',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nw',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nw',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nw',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nw',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nhx',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nhx',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nhx',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nhx',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nwk',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nwk',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nwk',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nwk',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'NEWICK2PHYLOXML': method gotree is not available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('newick',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('newick',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nw',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nw',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nhx',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nhx',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nwk',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nwk',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'NEXUS2CLUSTAL': method goalign is not available WARNING [bioconvert.core.base:152]: converter 'NEXUS2CLUSTAL': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'NEXUS2FASTA': method goalign is not available WARNING [bioconvert.core.base:152]: converter 'NEXUS2FASTA': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'NEXUS2NEWICK': method gotree is not available WARNING [bioconvert.core.base:152]: converter 'NEXUS2PHYLIP': method goalign is not available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nexus',) -> ('phy',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nexus',) -> ('ph',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nexus',) -> ('phylip',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nx',) -> ('phy',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nx',) -> ('ph',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nx',) -> ('phylip',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nex',) -> ('phy',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nex',) -> ('ph',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nex',) -> ('phylip',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nxs',) -> ('phy',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nxs',) -> ('ph',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nxs',) -> ('phylip',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'NEXUS2PHYLOXML': method gotree is not available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nexus',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nexus',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nx',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nx',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nex',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nex',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nxs',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nxs',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'PHYLIP2CLUSTAL': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'PHYLIP2FASTA': method goalign is not available WARNING [bioconvert.core.base:152]: converter 'PHYLIP2FASTA': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'PHYLIP2NEXUS': method goalign is not available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phy',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phy',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phy',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phy',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('ph',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('ph',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('ph',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('ph',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phylip',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phylip',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phylip',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phylip',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'PHYLIP2STOCKHOLM': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'PHYLOXML2NEWICK': method gotree is not available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('phyloxml',) -> ('newick',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('phyloxml',) -> ('nw',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('phyloxml',) -> ('nhx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('phyloxml',) -> ('nwk',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('xml',) -> ('newick',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('xml',) -> ('nw',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('xml',) -> ('nhx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('xml',) -> ('nwk',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'PHYLOXML2NEXUS': method gotree is not available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('phyloxml',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('phyloxml',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('phyloxml',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('phyloxml',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('xml',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('xml',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('xml',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('xml',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'PLINK2BPLINK': method plink is not available WARNING [bioconvert.core.registry:117]: converter 'PLINK2BPLINK' for ('plink',) -> ('bplink',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'PLINK2VCF': method plink is not available WARNING [bioconvert.core.registry:117]: converter 'PLINK2VCF' for ('plink',) -> ('vcf',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'SAM2BAM': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'SAM2BAM' for ('sam',) -> ('bam',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'SAM2CRAM': method samtools is not available WARNING [bioconvert.core.registry:117]: converter 'SAM2CRAM' for ('sam',) -> ('cram',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'STOCKHOLM2CLUSTAL': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'STOCKHOLM2PHYLIP': method squizz is not available WARNING [bioconvert.core.base:152]: converter 'VCF2BCF': method bcftools is not available WARNING [bioconvert.core.registry:117]: converter 'VCF2BCF' for ('vcf',) -> ('bcf',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'VCF2BPLINK': method plink is not available WARNING [bioconvert.core.registry:117]: converter 'VCF2BPLINK' for ('vcf',) -> ('bplink',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'VCF2PLINK': method plink is not available WARNING [bioconvert.core.registry:117]: converter 'VCF2PLINK' for ('vcf',) -> ('plink',) was not added as no method is available WARNING [bioconvert.core.base:152]: converter 'VCF2WIGGLE': method wiggletools is not available WARNING [bioconvert.core.registry:117]: converter 'VCF2WIGGLE' for ('vcf',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'VCF2WIGGLE' for ('vcf',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2CRAM' for ('bam',) -> ('cram',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2FASTA' for ('bam',) -> ('fasta',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2FASTA' for ('bam',) -> ('fa',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2FASTA' for ('bam',) -> ('fst',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2JSON' for ('bam',) -> ('json',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2SAM' for ('bam',) -> ('sam',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2TSV' for ('bam',) -> ('tsv',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2WIGGLE' for ('bam',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BAM2WIGGLE' for ('bam',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BCF2VCF' for ('bcf',) -> ('vcf',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BCF2WIGGLE' for ('bcf',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BCF2WIGGLE' for ('bcf',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BED2WIGGLE' for ('bed',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BED2WIGGLE' for ('bed',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BEDGRAPH2WIGGLE' for ('bedgraph',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BEDGRAPH2WIGGLE' for ('bedgraph',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BEDGRAPH2WIGGLE' for ('bg',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BEDGRAPH2WIGGLE' for ('bg',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGBED2WIGGLE' for ('bb',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGBED2WIGGLE' for ('bb',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGBED2WIGGLE' for ('bigbed',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGBED2WIGGLE' for ('bigbed',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGWIG2WIGGLE' for ('bigwig',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGWIG2WIGGLE' for ('bigwig',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGWIG2WIGGLE' for ('bw',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BIGWIG2WIGGLE' for ('bw',) -> ('wiggle',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BPLINK2PLINK' for ('bplink',) -> ('plink',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'BPLINK2VCF' for ('bplink',) -> ('vcf',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clustal',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clustal',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clustal',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clustal',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('aln',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('aln',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('aln',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('aln',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clw',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clw',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clw',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CLUSTAL2NEXUS' for ('clw',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2BAM' for ('cram',) -> ('bam',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTA' for ('cram',) -> ('fasta',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTA' for ('cram',) -> ('fa',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTA' for ('cram',) -> ('fst',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTQ' for ('cram',) -> ('fastq',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2FASTQ' for ('cram',) -> ('fq',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'CRAM2SAM' for ('cram',) -> ('sam',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'DSRC2GZ' for ('dsrc',) -> ('gz',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fasta',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fasta',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fasta',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fasta',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fa',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fa',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fa',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fa',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fst',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fst',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fst',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'FASTA2NEXUS' for ('fst',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'GZ2DSRC' for ('gz',) -> ('dsrc',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('newick',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('newick',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('newick',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('newick',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nw',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nw',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nw',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nw',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nhx',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nhx',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nhx',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nhx',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nwk',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nwk',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nwk',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2NEXUS' for ('nwk',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('newick',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('newick',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nw',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nw',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nhx',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nhx',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nwk',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEWICK2PHYLOXML' for ('nwk',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nexus',) -> ('phy',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nexus',) -> ('ph',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nexus',) -> ('phylip',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nx',) -> ('phy',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nx',) -> ('ph',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nx',) -> ('phylip',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nex',) -> ('phy',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nex',) -> ('ph',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nex',) -> ('phylip',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nxs',) -> ('phy',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nxs',) -> ('ph',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLIP' for ('nxs',) -> ('phylip',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nexus',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nexus',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nx',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nx',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nex',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nex',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nxs',) -> ('phyloxml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'NEXUS2PHYLOXML' for ('nxs',) -> ('xml',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phy',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phy',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phy',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phy',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('ph',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('ph',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('ph',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('ph',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phylip',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phylip',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phylip',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLIP2NEXUS' for ('phylip',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('phyloxml',) -> ('newick',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('phyloxml',) -> ('nw',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('phyloxml',) -> ('nhx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('phyloxml',) -> ('nwk',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('xml',) -> ('newick',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('xml',) -> ('nw',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('xml',) -> ('nhx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEWICK' for ('xml',) -> ('nwk',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('phyloxml',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('phyloxml',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('phyloxml',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('phyloxml',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('xml',) -> ('nexus',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('xml',) -> ('nx',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('xml',) -> ('nex',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PHYLOXML2NEXUS' for ('xml',) -> ('nxs',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PLINK2BPLINK' for ('plink',) -> ('bplink',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'PLINK2VCF' for ('plink',) -> ('vcf',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'SAM2BAM' for ('sam',) -> ('bam',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'SAM2CRAM' for ('sam',) -> ('cram',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'VCF2BCF' for ('vcf',) -> ('bcf',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'VCF2BPLINK' for ('vcf',) -> ('bplink',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'VCF2PLINK' for ('vcf',) -> ('plink',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'VCF2WIGGLE' for ('vcf',) -> ('wig',) was not added as no method is available WARNING [bioconvert.core.registry:117]: converter 'VCF2WIGGLE' for ('vcf',) -> ('wiggle',) was not added as no method is available

What you think might have happened

version issue when using the tool XXX

Please help.

cokelaer commented 2 years ago

Thanks for reporting this issue. Installing the third-party dependencies should remove the warnings. However, I agree this is a annoying and we plan to remove them in the release 0.5.0