[2024-01-24 12:39:41,908] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b0d760b-38fb-4462-ad2e-deb90c925296/dqc_reference
[2024-01-24 12:39:43,350] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,351] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,351] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4e85e77-118d-4142-9b68-14f80a548a85/GCF_001045435.1_ASM104543v1_genomic.fna.gz | prodigal -d GCF_001045435.1_ASM104543v1_genomic.fna/cds.fna -a GCF_001045435.1_ASM104543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:59,667] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:59,668] [INFO] Task started: HMMsearch
[2024-01-24 12:39:59,668] [INFO] Running command: hmmsearch --tblout GCF_001045435.1_ASM104543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b0d760b-38fb-4462-ad2e-deb90c925296/dqc_reference/reference_markers.hmm GCF_001045435.1_ASM104543v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:59,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:59,923] [INFO] Found 6/6 markers.
[2024-01-24 12:39:59,956] [INFO] Query marker FASTA was written to GCF_001045435.1_ASM104543v1_genomic.fna/markers.fasta
[2024-01-24 12:39:59,957] [INFO] Task started: Blastn
[2024-01-24 12:39:59,957] [INFO] Running command: blastn -query GCF_001045435.1_ASM104543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b0d760b-38fb-4462-ad2e-deb90c925296/dqc_reference/reference_markers.fasta -out GCF_001045435.1_ASM104543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:00,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:00,671] [INFO] Selected 15 target genomes.
[2024-01-24 12:40:00,671] [INFO] Target genome list was writen to GCF_001045435.1_ASM104543v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:00,677] [INFO] Task started: fastANI
[2024-01-24 12:40:00,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e85e77-118d-4142-9b68-14f80a548a85/GCF_001045435.1_ASM104543v1_genomic.fna.gz --refList GCF_001045435.1_ASM104543v1_genomic.fna/target_genomes.txt --output GCF_001045435.1_ASM104543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:09,512] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:09,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b0d760b-38fb-4462-ad2e-deb90c925296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:09,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b0d760b-38fb-4462-ad2e-deb90c925296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:09,524] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:09,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:09,525] [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
Chryseobacterium koreense	strain=CCUG 49689	GCA_001045435.1	232216	232216	type	True	100.0	1016	1017	95	conclusive
Chryseobacterium koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	99.9772	1002	1017	95	conclusive
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	77.951	288	1017	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.9213	251	1017	95	below_threshold
Kaistella treverensis	strain=DSM 22251	GCA_900114045.1	631455	631455	type	True	77.9128	209	1017	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.9083	252	1017	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.4871	231	1017	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	77.464	258	1017	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	77.422	254	1017	95	below_threshold
Chryseobacterium hispalense	strain=DSM 25574	GCA_000708615.2	1453492	1453492	type	True	77.3452	139	1017	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_900112115.1	266749	266749	type	True	77.3222	258	1017	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	77.2143	238	1017	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	76.8492	154	1017	95	below_threshold
Epilithonimonas xixisoli	strain=CGMCC 1.12802	GCA_004365655.1	1476462	1476462	type	True	76.7118	134	1017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:09,526] [INFO] DFAST Taxonomy check result was written to GCF_001045435.1_ASM104543v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:09,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:09,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:09,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b0d760b-38fb-4462-ad2e-deb90c925296/dqc_reference/checkm_data
[2024-01-24 12:40:09,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:09,560] [INFO] Task started: CheckM
[2024-01-24 12:40:09,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001045435.1_ASM104543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001045435.1_ASM104543v1_genomic.fna/checkm_input GCF_001045435.1_ASM104543v1_genomic.fna/checkm_result
[2024-01-24 12:40:57,925] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:57,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:57,947] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:57,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:57,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001045435.1_ASM104543v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:57,948] [INFO] Task started: Blastn
[2024-01-24 12:40:57,948] [INFO] Running command: blastn -query GCF_001045435.1_ASM104543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b0d760b-38fb-4462-ad2e-deb90c925296/dqc_reference/reference_markers_gtdb.fasta -out GCF_001045435.1_ASM104543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:58,750] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:58,758] [INFO] Selected 15 target genomes.
[2024-01-24 12:40:58,758] [INFO] Target genome list was writen to GCF_001045435.1_ASM104543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:58,771] [INFO] Task started: fastANI
[2024-01-24 12:40:58,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e85e77-118d-4142-9b68-14f80a548a85/GCF_001045435.1_ASM104543v1_genomic.fna.gz --refList GCF_001045435.1_ASM104543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001045435.1_ASM104543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:06,135] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:06,158] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:06,158] [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_001045435.1	s__Kaistella koreensis	100.0	1016	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCA_002426785.1	s__Kaistella sp002426785	79.0174	375	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
GCF_000735695.2	s__Kaistella haifensis	78.8443	311	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.72	96.43	0.83	0.82	4	-
GCF_907163125.1	s__Cloacibacterium caeni_B	78.8427	119	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	N/A	N/A	N/A	N/A	1	-
GCF_001403755.1	s__Kaistella senegalense	78.4519	251	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898255.1	s__Kaistella sp001898255	78.276	268	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.97	99.97	0.99	0.99	2	-
GCF_002205795.1	s__Kaistella sp002205795	78.202	254	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	95.66	95.02	0.89	0.88	3	-
GCA_002453895.1	s__Kaistella sp002453895	78.192	283	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002197835.1	s__Kaistella sp002197835	78.0772	303	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.62	97.62	0.94	0.94	2	-
GCA_015999765.1	s__Kaistella sp015999765	77.9995	255	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCF_900156725.1	s__Kaistella chaponensis	77.9585	288	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019195395.1	s__Kaistella sp019195395	77.8865	253	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907163105.1	s__Cloacibacterium caeni_A	77.8139	112	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014695.1	s__Kaistella sp008014695	77.4867	184	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365655.1	s__Epilithonimonas xixisoli	76.7118	134	1017	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:06,160] [INFO] GTDB search result was written to GCF_001045435.1_ASM104543v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:06,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:06,164] [INFO] DFAST_QC result json was written to GCF_001045435.1_ASM104543v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:06,164] [INFO] DFAST_QC completed!
[2024-01-24 12:41:06,164] [INFO] Total running time: 0h1m24s