Output files

The output folder of the lineage_wf and taxonomy_wf workflows contains:

File	Description
quality_report.tsv	Completeness, contamination, strain heterogeneity and genome statistics of each bin: the tab-separated table produced by qa -o 2 --tab_table (see Reported statistics).
lineage.ms.gz or <taxon>.ms.gz	Marker file used to assess the bins (see lineage_set and taxon_set).
checkm.log	Log of the commands run on the output folder.
bins/<bin id>/	Called genes (genes.faa.gz, genes.gff.gz, and genes.fna.gz with --nt) and HMMER results (hmmer.tree.txt.gz, hmmer.analyze.txt.gz, and the *.ali.txt.gz alignments with --ali) of each bin.
storage/	Genome statistics (bin_stats.tree.tsv.gz, bin_stats.analyze.tsv.gz, bin_stats_ext.tsv.gz), marker gene positions (marker_gene_stats.tsv.gz), alignments of marker genes found multiple times in a bin (aai_qa.tar.gz, used to calculate strain heterogeneity), and HMM information (*.pkl.gz).
storage/tree/	Placement of the bins in the reference genome tree (lineage_wf only): marker gene alignments (<marker>.masked.faa.gz), the concatenated alignment (concatenated.fasta.gz), gPlace’s placements (concatenated.pplacer.json.gz) and tree (concatenated.tre.gz), and gPlace’s logs (pplacer.out, gplace.log, gplace.warnings.log).

The bins and storage folders are needed to re-run qa and the plotting commands on the output folder. Use --rm_tmp_files to remove them once a workflow has finished if only quality_report.tsv is needed.

Compressed files

From CheckM 1.3.0, most output files are gzip-compressed, which makes the output folder ~3.5 times smaller (e.g., 1.2 GB instead of 4.4 GB for 1,000 genomes). They can be read with standard tools, e.g.:

zcat ./output/storage/bin_stats_ext.tsv.gz | head
tar -tzf ./output/storage/aai_qa.tar.gz

CheckM commands read both compressed outputs and the uncompressed outputs of CheckM <= 1.2.10, and accept file names without the .gz extension (e.g., checkm qa ./output/lineage.ms ./output). If both a compressed and an uncompressed marker file exist (e.g., lineage.ms and lineage.ms.gz in an output folder reused from an earlier version of CheckM), the most recently modified file is used.

Note

CheckM <= 1.2.10 wrote these files uncompressed (e.g., lineage.ms, bins/<bin id>/genes.faa and storage/bin_stats_ext.tsv) and stored the alignments used to calculate strain heterogeneity in the storage/aai_qa folder. Scripts that read these files directly need to be updated for CheckM >= 1.3.0.