[2024-01-25 17:48:20,801] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:20,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:20,803] [INFO] DQC Reference Directory: /var/lib/cwl/stge2901593-040f-42c2-93d1-ee922e55606d/dqc_reference
[2024-01-25 17:48:21,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:21,925] [INFO] Task started: Prodigal
[2024-01-25 17:48:21,925] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8eb6fa9-793e-4706-976c-ed4ddd2c2c9a/GCF_003054025.1_ASM305402v1_genomic.fna.gz | prodigal -d GCF_003054025.1_ASM305402v1_genomic.fna/cds.fna -a GCF_003054025.1_ASM305402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:30,392] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:30,392] [INFO] Task started: HMMsearch
[2024-01-25 17:48:30,392] [INFO] Running command: hmmsearch --tblout GCF_003054025.1_ASM305402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2901593-040f-42c2-93d1-ee922e55606d/dqc_reference/reference_markers.hmm GCF_003054025.1_ASM305402v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:30,602] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:30,603] [INFO] Found 6/6 markers.
[2024-01-25 17:48:30,644] [INFO] Query marker FASTA was written to GCF_003054025.1_ASM305402v1_genomic.fna/markers.fasta
[2024-01-25 17:48:30,645] [INFO] Task started: Blastn
[2024-01-25 17:48:30,645] [INFO] Running command: blastn -query GCF_003054025.1_ASM305402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2901593-040f-42c2-93d1-ee922e55606d/dqc_reference/reference_markers.fasta -out GCF_003054025.1_ASM305402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:31,210] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:31,213] [INFO] Selected 16 target genomes.
[2024-01-25 17:48:31,213] [INFO] Target genome list was writen to GCF_003054025.1_ASM305402v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:31,222] [INFO] Task started: fastANI
[2024-01-25 17:48:31,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8eb6fa9-793e-4706-976c-ed4ddd2c2c9a/GCF_003054025.1_ASM305402v1_genomic.fna.gz --refList GCF_003054025.1_ASM305402v1_genomic.fna/target_genomes.txt --output GCF_003054025.1_ASM305402v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:40,597] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:40,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2901593-040f-42c2-93d1-ee922e55606d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:40,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2901593-040f-42c2-93d1-ee922e55606d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:40,604] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:40,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:40,604] [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
Capnocytophaga leadbetteri	strain=DSM 22902	GCA_003054025.1	327575	327575	type	True	100.0	855	859	95	conclusive
Capnocytophaga endodontalis	strain=ChDC OS43	GCA_002209445.1	2708117	2708117	type	True	81.4128	445	859	95	below_threshold
Capnocytophaga sputigena	strain=NCTC11653	GCA_900446695.1	1019	1019	type	True	81.2114	424	859	95	below_threshold
Capnocytophaga periodontitidis	strain=p1a2	GCA_016126015.1	2795027	2795027	type	True	81.023	422	859	95	below_threshold
Capnocytophaga bilenii	strain=Marseille-Q4570	GCA_017565765.1	2819369	2819369	type	True	80.9255	377	859	95	below_threshold
Capnocytophaga ochracea	strain=FDAARGOS_1468	GCA_019930725.1	1018	1018	type	True	79.4347	373	859	95	below_threshold
Capnocytophaga ochracea	strain=DSM 7271	GCA_000023285.1	1018	1018	type	True	79.3506	374	859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:40,606] [INFO] DFAST Taxonomy check result was written to GCF_003054025.1_ASM305402v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:40,606] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:40,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:40,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2901593-040f-42c2-93d1-ee922e55606d/dqc_reference/checkm_data
[2024-01-25 17:48:40,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:40,636] [INFO] Task started: CheckM
[2024-01-25 17:48:40,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003054025.1_ASM305402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003054025.1_ASM305402v1_genomic.fna/checkm_input GCF_003054025.1_ASM305402v1_genomic.fna/checkm_result
[2024-01-25 17:49:08,039] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:08,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:08,068] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:08,068] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:08,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003054025.1_ASM305402v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:08,069] [INFO] Task started: Blastn
[2024-01-25 17:49:08,069] [INFO] Running command: blastn -query GCF_003054025.1_ASM305402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2901593-040f-42c2-93d1-ee922e55606d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003054025.1_ASM305402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:08,860] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:08,862] [INFO] Selected 16 target genomes.
[2024-01-25 17:49:08,862] [INFO] Target genome list was writen to GCF_003054025.1_ASM305402v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:08,876] [INFO] Task started: fastANI
[2024-01-25 17:49:08,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8eb6fa9-793e-4706-976c-ed4ddd2c2c9a/GCF_003054025.1_ASM305402v1_genomic.fna.gz --refList GCF_003054025.1_ASM305402v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003054025.1_ASM305402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:18,543] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:18,549] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:18,549] [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_003054025.1	s__Capnocytophaga leadbetteri	100.0	855	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	95.46	95.36	0.86	0.85	6	conclusive
GCF_002209445.1	s__Capnocytophaga endodontalis	81.387	447	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.66	96.51	0.90	0.87	9	-
GCF_900446695.1	s__Capnocytophaga sputigena	81.243	422	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.52	96.32	0.92	0.88	8	-
GCF_002999135.1	s__Capnocytophaga sp002999135	81.042	366	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565765.1	s__Capnocytophaga bilenii	80.9504	375	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.25	97.25	0.91	0.91	2	-
GCF_000023285.1	s__Capnocytophaga ochracea	79.3918	372	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.34	96.09	0.90	0.87	17	-
GCF_002302635.1	s__Capnocytophaga stomatis	76.9822	76	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.71	97.65	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:18,550] [INFO] GTDB search result was written to GCF_003054025.1_ASM305402v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:18,550] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:18,552] [INFO] DFAST_QC result json was written to GCF_003054025.1_ASM305402v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:18,553] [INFO] DFAST_QC completed!
[2024-01-25 17:49:18,553] [INFO] Total running time: 0h0m58s