[2024-01-24 13:17:47,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:47,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:47,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgb024a4f0-7ba4-4dd4-86be-b67e299105ea/dqc_reference
[2024-01-24 13:17:48,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:48,480] [INFO] Task started: Prodigal
[2024-01-24 13:17:48,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg06707ff2-e4cf-4808-82b1-db70024b3421/GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/cds.fna -a GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:59,655] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:59,656] [INFO] Task started: HMMsearch
[2024-01-24 13:17:59,656] [INFO] Running command: hmmsearch --tblout GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb024a4f0-7ba4-4dd4-86be-b67e299105ea/dqc_reference/reference_markers.hmm GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:59,989] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:59,991] [INFO] Found 6/6 markers.
[2024-01-24 13:18:00,024] [INFO] Query marker FASTA was written to GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:18:00,025] [INFO] Task started: Blastn
[2024-01-24 13:18:00,025] [INFO] Running command: blastn -query GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb024a4f0-7ba4-4dd4-86be-b67e299105ea/dqc_reference/reference_markers.fasta -out GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:00,749] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:00,752] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:00,753] [INFO] Target genome list was writen to GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:18:00,757] [INFO] Task started: fastANI
[2024-01-24 13:18:00,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg06707ff2-e4cf-4808-82b1-db70024b3421/GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna.gz --refList GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:07,800] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:07,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb024a4f0-7ba4-4dd4-86be-b67e299105ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:07,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb024a4f0-7ba4-4dd4-86be-b67e299105ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:07,812] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:07,812] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:07,812] [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
Empedobacter tilapiae	strain=MRS2	GCA_004785645.1	2491114	2491114	type	True	82.9262	706	1065	95	below_threshold
Empedobacter brevis	strain=ATCC 43319	GCA_000382425.1	247	247	type	True	81.7098	658	1065	95	below_threshold
Empedobacter brevis	strain=NBRC 14943	GCA_007990795.1	247	247	type	True	81.6032	647	1065	95	below_threshold
Chishuiella changwenlii	strain=DSM 27989	GCA_900142565.1	1434701	1434701	type	True	81.1716	614	1065	95	below_threshold
Chishuiella changwenlii	strain=CGMCC 1.12707	GCA_014638465.1	1434701	1434701	type	True	81.1418	610	1065	95	below_threshold
Faecalibacter macacae	strain=YIM 102668	GCA_003687725.1	1859289	1859289	type	True	79.5619	493	1065	95	below_threshold
Faecalibacter bovis	strain=ZY171143	GCA_017948305.1	2898187	2898187	type	True	79.5512	477	1065	95	below_threshold
Faecalibacter rhinopitheci	strain=WQ 117	GCA_015234135.1	2779678	2779678	type	True	79.3518	434	1065	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.0764	60	1065	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	75.6933	77	1065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:07,814] [INFO] DFAST Taxonomy check result was written to GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:18:07,815] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:07,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:07,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb024a4f0-7ba4-4dd4-86be-b67e299105ea/dqc_reference/checkm_data
[2024-01-24 13:18:07,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:07,854] [INFO] Task started: CheckM
[2024-01-24 13:18:07,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/checkm_input GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:18:44,510] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:44,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:44,542] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:44,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:44,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:18:44,543] [INFO] Task started: Blastn
[2024-01-24 13:18:44,544] [INFO] Running command: blastn -query GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb024a4f0-7ba4-4dd4-86be-b67e299105ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:45,435] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:45,438] [INFO] Selected 6 target genomes.
[2024-01-24 13:18:45,438] [INFO] Target genome list was writen to GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:45,445] [INFO] Task started: fastANI
[2024-01-24 13:18:45,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg06707ff2-e4cf-4808-82b1-db70024b3421/GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna.gz --refList GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:50,540] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:50,552] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:50,553] [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_900115015.1	s__Algoriella xinjiangensis	100.0	1062	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Algoriella	95.0	98.62	97.69	0.94	0.93	3	conclusive
GCF_013488205.1	s__Empedobacter falsenii_A	82.9937	749	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.19	95.74	0.91	0.86	9	-
GCA_002378465.1	s__Empedobacter sp002378465	82.9851	696	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.64	95.90	0.90	0.86	24	-
GCF_004785645.1	s__Empedobacter tilapiae	82.9249	705	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013116755.1	s__Empedobacter stercoris	82.5132	645	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	99.07	99.07	0.96	0.96	2	-
GCF_900142565.1	s__Chishuiella changwenlii	81.172	614	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:50,554] [INFO] GTDB search result was written to GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:50,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:50,652] [INFO] DFAST_QC result json was written to GCF_900115015.1_IMG-taxon_2675903033_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:18:50,653] [INFO] DFAST_QC completed!
[2024-01-24 13:18:50,653] [INFO] Total running time: 0h1m4s