[2024-01-24 13:12:52,325] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,329] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,329] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1bd83ab-ca53-408d-b832-03642659d642/dqc_reference
[2024-01-24 13:12:53,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:53,622] [INFO] Task started: Prodigal
[2024-01-24 13:12:53,622] [INFO] Running command: gunzip -c /var/lib/cwl/stgd10ae895-7f4e-4ceb-9799-c006907da235/GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/cds.fna -a GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:57,444] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:57,444] [INFO] Task started: HMMsearch
[2024-01-24 13:12:57,444] [INFO] Running command: hmmsearch --tblout GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1bd83ab-ca53-408d-b832-03642659d642/dqc_reference/reference_markers.hmm GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:57,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:57,774] [INFO] Found 6/6 markers.
[2024-01-24 13:12:57,793] [INFO] Query marker FASTA was written to GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:12:57,794] [INFO] Task started: Blastn
[2024-01-24 13:12:57,794] [INFO] Running command: blastn -query GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1bd83ab-ca53-408d-b832-03642659d642/dqc_reference/reference_markers.fasta -out GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:58,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:58,409] [INFO] Selected 25 target genomes.
[2024-01-24 13:12:58,410] [INFO] Target genome list was writen to GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:12:58,471] [INFO] Task started: fastANI
[2024-01-24 13:12:58,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgd10ae895-7f4e-4ceb-9799-c006907da235/GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna.gz --refList GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:08,219] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:08,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1bd83ab-ca53-408d-b832-03642659d642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:08,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1bd83ab-ca53-408d-b832-03642659d642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:08,224] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:08,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:08,225] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Atopostipes suicloacalis	strain=DSM 15692	GCA_900129085.1	180295	180295	type	True	100.0	679	682	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:13:08,226] [INFO] DFAST Taxonomy check result was written to GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:13:08,227] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:08,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:08,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1bd83ab-ca53-408d-b832-03642659d642/dqc_reference/checkm_data
[2024-01-24 13:13:08,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:08,265] [INFO] Task started: CheckM
[2024-01-24 13:13:08,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/checkm_input GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:13:28,042] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:28,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:28,065] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:28,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:28,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:13:28,066] [INFO] Task started: Blastn
[2024-01-24 13:13:28,066] [INFO] Running command: blastn -query GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1bd83ab-ca53-408d-b832-03642659d642/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:28,858] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:28,861] [INFO] Selected 21 target genomes.
[2024-01-24 13:13:28,862] [INFO] Target genome list was writen to GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:28,883] [INFO] Task started: fastANI
[2024-01-24 13:13:28,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgd10ae895-7f4e-4ceb-9799-c006907da235/GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna.gz --refList GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:36,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:36,671] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:36,671] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900129085.1	s__Atopostipes suicloacalis	100.0	679	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Atopostipes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019116785.1	s__Atopostipes pullistercoris	84.981	420	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Atopostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588235.1	s__Atopostipes sp910588235	78.2834	154	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Atopostipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:36,673] [INFO] GTDB search result was written to GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:36,674] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:36,677] [INFO] DFAST_QC result json was written to GCF_900129085.1_IMG-taxon_2582581273_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:13:36,677] [INFO] DFAST_QC completed!
[2024-01-24 13:13:36,677] [INFO] Total running time: 0h0m44s