[2024-01-24 13:49:19,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,458] [INFO] DQC Reference Directory: /var/lib/cwl/stge8ec2e54-a54a-4024-99e1-9cf859008f9a/dqc_reference
[2024-01-24 13:49:20,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,754] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,755] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfa62cf8-2de3-47e4-80ae-1c5b693a5f75/GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/cds.fna -a GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,560] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,560] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,560] [INFO] Running command: hmmsearch --tblout GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8ec2e54-a54a-4024-99e1-9cf859008f9a/dqc_reference/reference_markers.hmm GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:42,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:42,858] [INFO] Found 6/6 markers.
[2024-01-24 13:49:42,892] [INFO] Query marker FASTA was written to GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:42,892] [INFO] Task started: Blastn
[2024-01-24 13:49:42,893] [INFO] Running command: blastn -query GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge8ec2e54-a54a-4024-99e1-9cf859008f9a/dqc_reference/reference_markers.fasta -out GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,653] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,657] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:43,657] [INFO] Target genome list was writen to GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,664] [INFO] Task started: fastANI
[2024-01-24 13:49:43,664] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfa62cf8-2de3-47e4-80ae-1c5b693a5f75/GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna.gz --refList GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:00,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8ec2e54-a54a-4024-99e1-9cf859008f9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:00,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8ec2e54-a54a-4024-99e1-9cf859008f9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:00,215] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:00,215] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:00,216] [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
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	100.0	1362	1363	95	conclusive
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	82.2573	775	1363	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	82.1379	687	1363	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	80.9169	615	1363	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	79.938	633	1363	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	79.6478	467	1363	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	79.3448	408	1363	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	79.3038	443	1363	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	79.2623	411	1363	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.226	492	1363	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	78.7819	384	1363	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	78.5492	351	1363	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	78.5153	362	1363	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.3495	357	1363	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.3283	337	1363	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.3035	348	1363	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.057	355	1363	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.0822	140	1363	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,218] [INFO] DFAST Taxonomy check result was written to GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:00,219] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:00,219] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:00,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8ec2e54-a54a-4024-99e1-9cf859008f9a/dqc_reference/checkm_data
[2024-01-24 13:50:00,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:00,269] [INFO] Task started: CheckM
[2024-01-24 13:50:00,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/checkm_input GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:51:01,721] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:01,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:01,741] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:01,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:01,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:51:01,742] [INFO] Task started: Blastn
[2024-01-24 13:51:01,742] [INFO] Running command: blastn -query GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge8ec2e54-a54a-4024-99e1-9cf859008f9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:02,661] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:02,665] [INFO] Selected 12 target genomes.
[2024-01-24 13:51:02,665] [INFO] Target genome list was writen to GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:02,689] [INFO] Task started: fastANI
[2024-01-24 13:51:02,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfa62cf8-2de3-47e4-80ae-1c5b693a5f75/GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna.gz --refList GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:12,811] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:12,825] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:12,825] [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_900129545.1	s__Flavobacterium fluvii	100.0	1362	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014379405.1	s__Flavobacterium sp014379405	86.268	860	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989775.1	s__Flavobacterium sp017989775	84.8059	421	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.62	98.46	0.76	0.72	3	-
GCA_013823965.1	s__Flavobacterium sp013823965	83.3701	681	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	82.2688	774	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	82.1464	686	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCF_015277675.1	s__Flavobacterium soyangense	81.2819	584	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365135.1	s__Flavobacterium sp010365135	81.2776	572	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355225.1	s__Flavobacterium nackdongense	80.9236	614	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861155.1	s__Flavobacterium sp903861155	80.572	495	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCF_002797935.1	s__Flavobacterium sp002797935	79.7396	522	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813295.1	s__Flavobacterium sp002813295	79.3296	417	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:12,829] [INFO] GTDB search result was written to GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:12,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:12,835] [INFO] DFAST_QC result json was written to GCF_900129545.1_IMG-taxon_2695420956_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:51:12,835] [INFO] DFAST_QC completed!
[2024-01-24 13:51:12,835] [INFO] Total running time: 0h1m53s