bernt-matthias
commented
3 months ago Do you have a test history for this?
Closed jennaj closed 3 months ago
bernt-matthias
commented
3 months ago Do you have a test history for this?
mvdbeek
commented
3 months ago There's been a change of the API response, I'm afraid the fix is always going to be to update the tool. Maybe we can ask for a little more stability there. See also the failing weekly tests:
Job in error state.. tool_id: datasets_download_genome, exit_code: 1, stderr: New version of client (16.18.1) available at https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets.
Warning - included annotation files cover whole genome even though chromosome fasta was selected
dataformat doesn't recognize this input
For best results
1. Make sure to use --as-json-lines with the datasets command
2. Make sure that you're using the latest version of the datasets command line tool
Use --force to remove this warning.
Download the latest version of the datasets command line tool: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install
Error: unknown field "devStage"
Usage
dataformat tsv genome [flags]
Examples
dataformat tsv genome --inputfile human/ncbi_dataset/data/assembly_data_report.jsonl
dataformat tsv genome --package human.zip
Flags
--fields strings Comma-separated list of fields (default accession,ani-best-ani-match-ani,ani-best-ani-match-assembly,ani-best-ani-match-assembly_coverage,ani-best-ani-match-category,ani-best-ani-match-organism,ani-best-ani-match-type_assembly_coverage,ani-best-match-status,ani-category,ani-check-status,ani-comment,ani-submitted-ani-match-ani,ani-submitted-ani-match-assembly,ani-submitted-ani-match-assembly_coverage,ani-submitted-ani-match-category,ani-submitted-ani-match-organism,ani-submitted-ani-match-type_assembly_coverage,ani-submitted-organism,ani-submitted-species,annotinfo-busco-complete,annotinfo-busco-duplicated,annotinfo-busco-fragmented,annotinfo-busco-lineage,annotinfo-busco-missing,annotinfo-busco-singlecopy,annotinfo-busco-totalcount,annotinfo-busco-ver,annotinfo-featcount-gene-non-coding,annotinfo-featcount-gene-other,annotinfo-featcount-gene-protein-coding,annotinfo-featcount-gene-pseudogene,annotinfo-featcount-gene-total,annotinfo-method,annotinfo-name,annotinfo-pipeline,annotinfo-provider,annotinfo-release-date,annotinfo-release-version,annotinfo-report-url,annotinfo-software-version,annotinfo-status,assminfo-assembly-method,assminfo-atypicalis-atypical,assminfo-atypicalwarnings,assminfo-bioproject,assminfo-bioproject-lineage-accession,assminfo-bioproject-lineage-parent-accession,assminfo-bioproject-lineage-parent-accessions,assminfo-bioproject-lineage-title,assminfo-biosample-accession,assminfo-biosample-attribute-name,assminfo-biosample-attribute-value,assminfo-biosample-bioproject-accession,assminfo-biosample-bioproject-parent-accession,assminfo-biosample-bioproject-parent-accessions,assminfo-biosample-bioproject-title,assminfo-biosample-description-comment,assminfo-biosample-description-organism-common-name,assminfo-biosample-description-organism-infraspecific-breed,assminfo-biosample-description-organism-infraspecific-cultivar,assminfo-biosample-description-organism-infraspecific-ecotype,assminfo-biosample-description-organism-infraspecific-isolate,assminfo-biosample-description-organism-infraspecific-sex,assminfo-biosample-description-organism-infraspecific-strain,assminfo-biosample-description-organism-name,assminfo-biosample-description-organism-pangolin,assminfo-biosample-description-organism-tax-id,assminfo-biosample-description-title,assminfo-biosample-ids-db,assminfo-biosample-ids-label,assminfo-biosample-ids-value,assminfo-biosample-last-updated,assminfo-biosample-models,assminfo-biosample-owner-contact-lab,assminfo-biosample-owner-name,assminfo-biosample-package,assminfo-biosample-publication-date,assminfo-biosample-status-status,assminfo-biosample-status-when,assminfo-biosample-submission-date,assminfo-blast-url,assminfo-description,assminfo-level,assminfo-linked-assm-accession,assminfo-linked-assm-type,assminfo-name,assminfo-notes,assminfo-paired-assm-accession,assminfo-paired-assm-changed,assminfo-paired-assm-manual-diff,assminfo-paired-assm-name,assminfo-paired-assm-only-genbank,assminfo-paired-assm-only-refseq,assminfo-paired-assm-status,assminfo-refseq-category,assminfo-release-date,assminfo-sequencing-tech,assminfo-status,assminfo-submitter,assminfo-suppression-reason,assminfo-synonym,assminfo-type,assmstats-contig-l50,assmstats-contig-n50,assmstats-gaps-between-scaffolds-count,assmstats-gc-count,assmstats-gc-percent,assmstats-genome-coverage,assmstats-number-of-component-sequences,assmstats-number-of-contigs,assmstats-number-of-organelles,assmstats-number-of-scaffolds,assmstats-scaffold-l50,assmstats-scaffold-n50,assmstats-total-number-of-chromosomes,assmstats-total-sequence-len,assmstats-total-ungapped-len,checkm-completeness,checkm-completeness-percentile,checkm-contamination,checkm-marker-set,checkm-marker-set-rank,checkm-species-tax-id,checkm-version,current-accession,organelle-assembly-name,organelle-bioproject-accessions,organelle-description,organelle-infraspecific-name,organelle-submitter,organelle-total-seq-length,organism-common-name,organism-infraspecific-breed,organism-infraspecific-cultivar,organism-infraspecific-ecotype,organism-infraspecific-isolate,organism-infraspecific-sex,organism-infraspecific-strain,organism-name,organism-pangolin,organism-tax-id,source_database,type_material-display_text,type_material-label,wgs-contigs-url,wgs-project-accession,wgs-url)
- accession
- ani-best-ani-match-ani
- ani-best-ani-match-assembly
- ani-best-ani-match-assembly_coverage
- ani-best-ani-match-category
- ani-best-ani-match-organism
- ani-best-ani-match-type_assembly_coverage
- ani-best-match-status
- ani-category
- ani-check-status
- ani-comment
- ani-submitted-ani-match-ani
- ani-submitted-ani-match-assembly
- ani-submitted-ani-match-assembly_coverage
- ani-submitted-ani-match-category
- ani-submitted-ani-match-organism
- ani-submitted-ani-match-type_assembly_coverage
- ani-submitted-organism
- ani-submitted-species
- annotinfo-busco-complete
- annotinfo-busco-duplicated
- annotinfo-busco-fragmented
- annotinfo-busco-lineage
- annotinfo-busco-missing
- annotinfo-busco-singlecopy
- annotinfo-busco-totalcount
- annotinfo-busco-ver
- annotinfo-featcount-gene-non-coding
- annotinfo-featcount-gene-other
- annotinfo-featcount-gene-protein-coding
- annotinfo-featcount-gene-pseudogene
- annotinfo-featcount-gene-total
- annotinfo-method
- annotinfo-name
- annotinfo-pipeline
- annotinfo-provider
- annotinfo-release-date
- annotinfo-release-version
- annotinfo-report-url
- annotinfo-software-version
- annotinfo-status
- assminfo-assembly-method
- assminfo-atypicalis-atypical
- assminfo-atypicalwarnings
- assminfo-bioproject
- assminfo-bioproject-lineage-accession
- assminfo-bioproject-lineage-parent-accession
- assminfo-bioproject-lineage-parent-accessions
- assminfo-bioproject-lineage-title
- assminfo-biosample-accession
- assminfo-biosample-attribute-name
- assminfo-biosample-attribute-value
- assminfo-biosample-bioproject-accession
- assminfo-biosample-bioproject-parent-accession
- assminfo-biosample-bioproject-parent-accessions
- assminfo-biosample-bioproject-title
- assminfo-biosample-description-comment
- assminfo-biosample-description-organism-common-name
- assminfo-biosample-description-organism-infraspecific-breed
- assminfo-biosample-description-organism-infraspecific-cultivar
- assminfo-biosample-description-organism-infraspecific-ecotype
- assminfo-biosample-description-organism-infraspecific-isolate
- assminfo-biosample-description-organism-infraspecific-sex
- assminfo-biosample-description-organism-infraspecific-strain
- assminfo-biosample-description-organism-name
- assminfo-biosample-description-organism-pangolin
- assminfo-biosample-description-organism-tax-id
- assminfo-biosample-description-title
- assminfo-biosample-ids-db
- assminfo-biosample-ids-label
- assminfo-biosample-ids-value
- assminfo-biosample-last-updated
- assminfo-biosample-models
- assminfo-biosample-owner-contact-lab
- assminfo-biosample-owner-name
- assminfo-biosample-package
- assminfo-biosample-publication-date
- assminfo-biosample-status-status
- assminfo-biosample-status-when
- assminfo-biosample-submission-date
- assminfo-blast-url
- assminfo-description
- assminfo-level
- assminfo-linked-assm-accession
- assminfo-linked-assm-type
- assminfo-name
- assminfo-notes
- assminfo-paired-assm-accession
- assminfo-paired-assm-changed
- assminfo-paired-assm-manual-diff
- assminfo-paired-assm-name
- assminfo-paired-assm-only-genbank
- assminfo-paired-assm-only-refseq
- assminfo-paired-assm-status
- assminfo-refseq-category
- assminfo-release-date
- assminfo-sequencing-tech
- assminfo-status
- assminfo-submitter
- assminfo-suppression-reason
- assminfo-synonym
- assminfo-type
- assmstats-contig-l50
- assmstats-contig-n50
- assmstats-gaps-between-scaffolds-count
- assmstats-gc-count
- assmstats-gc-percent
- assmstats-genome-coverage
- assmstats-number-of-component-sequences
- assmstats-number-of-contigs
- assmstats-number-of-organelles
- assmstats-number-of-scaffolds
- assmstats-scaffold-l50
- assmstats-scaffold-n50
- assmstats-total-number-of-chromosomes
- assmstats-total-sequence-len
- assmstats-total-ungapped-len
- checkm-completeness
- checkm-completeness-percentile
- checkm-contamination
- checkm-marker-set
- checkm-marker-set-rank
- checkm-species-tax-id
- checkm-version
- current-accession
- organelle-assembly-name
- organelle-bioproject-accessions
- organelle-description
- organelle-infraspecific-name
- organelle-submitter
- organelle-total-seq-length
- organism-common-name
- organism-infraspecific-breed
- organism-infraspecific-cultivar
- organism-infraspecific-ecotype
- organism-infraspecific-isolate
- organism-infraspecific-sex
- organism-infraspecific-strain
- organism-name
- organism-pangolin
- organism-tax-id
- source_database
- type_material-display_text
- type_material-label
- wgs-contigs-url
- wgs-project-accession
- wgs-url
-h, --help help for genome
--inputfile string Input file (default "ncbi_dataset/data/assembly_data_report.jsonl")
--package string Data package (zip archive), inputfile parameter is relative to the root path inside the archive
Global Flags
--elide-header Do not output header
--force Force dataformat to run without type check prompt
.I'm on the update.
Could you open an upstream issue?
Tool just recently stopped working as per end user reports. Maybe something at NCBI changed?
tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome/16.6.0+galaxy0
png @bernt-matthias since I saw that you last worked on this :) Thanks!