[2024-01-25 18:04:51,475] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:51,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:51,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c71366b-e3df-458e-a506-682f833bf13e/dqc_reference
[2024-01-25 18:04:52,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:52,641] [INFO] Task started: Prodigal
[2024-01-25 18:04:52,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e7026c2-46f4-4362-aed0-e63a9a443ddc/GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/cds.fna -a GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:59,477] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:59,477] [INFO] Task started: HMMsearch
[2024-01-25 18:04:59,478] [INFO] Running command: hmmsearch --tblout GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c71366b-e3df-458e-a506-682f833bf13e/dqc_reference/reference_markers.hmm GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:59,708] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:59,709] [INFO] Found 6/6 markers.
[2024-01-25 18:04:59,739] [INFO] Query marker FASTA was written to GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:04:59,739] [INFO] Task started: Blastn
[2024-01-25 18:04:59,740] [INFO] Running command: blastn -query GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c71366b-e3df-458e-a506-682f833bf13e/dqc_reference/reference_markers.fasta -out GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:00,379] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:00,385] [INFO] Selected 12 target genomes.
[2024-01-25 18:05:00,385] [INFO] Target genome list was writen to GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:05:00,396] [INFO] Task started: fastANI
[2024-01-25 18:05:00,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e7026c2-46f4-4362-aed0-e63a9a443ddc/GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna.gz --refList GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:05:09,316] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:09,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c71366b-e3df-458e-a506-682f833bf13e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:05:09,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c71366b-e3df-458e-a506-682f833bf13e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:05:09,325] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:05:09,325] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:05:09,325] [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
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.7712	338	784	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.8671	293	784	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.8472	236	784	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.7391	285	784	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.6706	292	784	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.491	284	784	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.4464	250	784	95	below_threshold
Streptomyces luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	76.1078	54	784	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	75.0847	54	784	95	below_threshold
Streptomyces flavovariabilis	strain=NRRL B-16367	GCA_000725785.1	284031	284031	type	True	75.021	50	784	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	74.9473	56	784	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	74.9209	52	784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:05:09,326] [INFO] DFAST Taxonomy check result was written to GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:05:09,327] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:05:09,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:05:09,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c71366b-e3df-458e-a506-682f833bf13e/dqc_reference/checkm_data
[2024-01-25 18:05:09,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:05:09,354] [INFO] Task started: CheckM
[2024-01-25 18:05:09,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/checkm_input GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:05:32,317] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:32,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:32,332] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:32,333] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:32,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:05:32,333] [INFO] Task started: Blastn
[2024-01-25 18:05:32,333] [INFO] Running command: blastn -query GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c71366b-e3df-458e-a506-682f833bf13e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:33,428] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:33,434] [INFO] Selected 11 target genomes.
[2024-01-25 18:05:33,434] [INFO] Target genome list was writen to GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:33,454] [INFO] Task started: fastANI
[2024-01-25 18:05:33,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e7026c2-46f4-4362-aed0-e63a9a443ddc/GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna.gz --refList GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:40,442] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:40,450] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:40,450] [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_900105025.1	s__Parafannyhessea umbonata	100.0	779	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	conclusive
GCF_012844235.1	s__Parafannyhessea sp900538935	93.4636	651	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	96.97	96.59	0.88	0.86	4	-
GCA_003862195.1	s__Parafannyhessea sp003862195	85.29	529	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCF_009695875.1	s__Olsenella_H porci	80.9578	329	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	97.87	97.72	0.91	0.87	6	-
GCA_902780325.1	s__Parafannyhessea sp902787335	80.8565	266	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCA_905214865.1	s__Olsenella_H sp905214865	80.8474	350	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	99.90	99.90	0.96	0.96	2	-
GCF_900111255.1	s__Parafannyhessea umbonata_A	80.2729	314	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	99.32	99.30	0.95	0.94	4	-
GCF_900120385.1	s__Olsenella_I phocaeensis	79.8852	292	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_I	95.0	97.88	97.64	0.87	0.85	3	-
GCF_000143845.1	s__Olsenella uli	79.7391	285	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
GCA_017459925.1	s__UBA9715 sp017459925	77.421	70	784	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851625.1	s__Streptomyces sp003851625	74.8958	64	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:40,452] [INFO] GTDB search result was written to GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:40,453] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:40,456] [INFO] DFAST_QC result json was written to GCF_900105025.1_IMG-taxon_2636416177_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:05:40,456] [INFO] DFAST_QC completed!
[2024-01-25 18:05:40,456] [INFO] Total running time: 0h0m49s