[2024-01-25 18:53:20,935] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:20,936] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:20,936] [INFO] DQC Reference Directory: /var/lib/cwl/stgc64eae6f-377f-4065-8fa1-df9977f49412/dqc_reference
[2024-01-25 18:53:22,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:22,172] [INFO] Task started: Prodigal
[2024-01-25 18:53:22,172] [INFO] Running command: gunzip -c /var/lib/cwl/stg03560345-e684-409c-871d-39bccd43753e/GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/cds.fna -a GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:38,091] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:38,091] [INFO] Task started: HMMsearch
[2024-01-25 18:53:38,091] [INFO] Running command: hmmsearch --tblout GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc64eae6f-377f-4065-8fa1-df9977f49412/dqc_reference/reference_markers.hmm GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:38,330] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:38,332] [INFO] Found 6/6 markers.
[2024-01-25 18:53:38,374] [INFO] Query marker FASTA was written to GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:53:38,374] [INFO] Task started: Blastn
[2024-01-25 18:53:38,375] [INFO] Running command: blastn -query GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc64eae6f-377f-4065-8fa1-df9977f49412/dqc_reference/reference_markers.fasta -out GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:39,011] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:39,014] [INFO] Selected 12 target genomes.
[2024-01-25 18:53:39,014] [INFO] Target genome list was writen to GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:53:39,020] [INFO] Task started: fastANI
[2024-01-25 18:53:39,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg03560345-e684-409c-871d-39bccd43753e/GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna.gz --refList GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:54,234] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:54,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc64eae6f-377f-4065-8fa1-df9977f49412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:54,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc64eae6f-377f-4065-8fa1-df9977f49412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:54,243] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:53:54,243] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:54,244] [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 anhuiense	strain=CGMCC 1.6859	GCA_900101855.1	459526	459526	suspected-type	True	100.0	1768	1772	95	conclusive
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	90.2064	1381	1772	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	89.4883	1398	1772	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	89.4198	1365	1772	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	89.4096	1411	1772	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	87.7124	1341	1772	95	below_threshold
Flavobacterium ginsenosidimutans	strain=THG 01	GCA_003254625.1	687844	687844	type	True	86.9975	1332	1772	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	85.7843	1310	1772	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	85.213	1220	1772	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.8495	1215	1772	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.2778	1078	1772	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.943	208	1772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:54,245] [INFO] DFAST Taxonomy check result was written to GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:53:54,246] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:54,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:54,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc64eae6f-377f-4065-8fa1-df9977f49412/dqc_reference/checkm_data
[2024-01-25 18:53:54,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:54,298] [INFO] Task started: CheckM
[2024-01-25 18:53:54,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/checkm_input GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:54:40,438] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:40,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:40,455] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:40,455] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:40,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:54:40,456] [INFO] Task started: Blastn
[2024-01-25 18:54:40,456] [INFO] Running command: blastn -query GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc64eae6f-377f-4065-8fa1-df9977f49412/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:41,394] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:41,397] [INFO] Selected 11 target genomes.
[2024-01-25 18:54:41,397] [INFO] Target genome list was writen to GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:41,409] [INFO] Task started: fastANI
[2024-01-25 18:54:41,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg03560345-e684-409c-871d-39bccd43753e/GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna.gz --refList GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:55,981] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:55,988] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:55,989] [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_900101855.1	s__Flavobacterium anhuiense	100.0	1768	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.61	97.43	0.90	0.88	4	conclusive
GCF_009826975.1	s__Flavobacterium sp009826975	94.9356	1490	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151235.1	s__Flavobacterium anhuiense_A	92.206	1450	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254545.1	s__Flavobacterium tistrianum	90.2064	1381	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	89.4991	1397	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	89.4197	1365	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735615.1	s__Flavobacterium sp016735615	89.1774	1357	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002303885.1	s__Flavobacterium sp002303885	87.7806	1339	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744675.1	s__Flavobacterium sp017744675	87.2722	1413	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112575.1	s__Flavobacterium phragmitis	85.7656	1313	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634245.1	s__Flavobacterium foetidum	83.5563	1074	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:55,991] [INFO] GTDB search result was written to GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:55,991] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:55,995] [INFO] DFAST_QC result json was written to GCF_900101855.1_IMG-taxon_2596583647_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:54:55,995] [INFO] DFAST_QC completed!
[2024-01-25 18:54:55,995] [INFO] Total running time: 0h1m35s