[2024-01-24 14:06:14,757] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg382225d0-6f1e-4c4f-97d7-c8d2811ee515/dqc_reference
[2024-01-24 14:06:16,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:16,164] [INFO] Task started: Prodigal
[2024-01-24 14:06:16,164] [INFO] Running command: gunzip -c /var/lib/cwl/stga7a84ea3-3799-4c30-9a98-8978fff492d8/GCF_003097635.1_ASM309763v1_genomic.fna.gz | prodigal -d GCF_003097635.1_ASM309763v1_genomic.fna/cds.fna -a GCF_003097635.1_ASM309763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:30,715] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:30,716] [INFO] Task started: HMMsearch
[2024-01-24 14:06:30,716] [INFO] Running command: hmmsearch --tblout GCF_003097635.1_ASM309763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg382225d0-6f1e-4c4f-97d7-c8d2811ee515/dqc_reference/reference_markers.hmm GCF_003097635.1_ASM309763v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:30,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:30,997] [INFO] Found 6/6 markers.
[2024-01-24 14:06:31,032] [INFO] Query marker FASTA was written to GCF_003097635.1_ASM309763v1_genomic.fna/markers.fasta
[2024-01-24 14:06:31,032] [INFO] Task started: Blastn
[2024-01-24 14:06:31,032] [INFO] Running command: blastn -query GCF_003097635.1_ASM309763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg382225d0-6f1e-4c4f-97d7-c8d2811ee515/dqc_reference/reference_markers.fasta -out GCF_003097635.1_ASM309763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:31,803] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:31,807] [INFO] Selected 26 target genomes.
[2024-01-24 14:06:31,807] [INFO] Target genome list was writen to GCF_003097635.1_ASM309763v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:31,821] [INFO] Task started: fastANI
[2024-01-24 14:06:31,822] [INFO] Running command: fastANI --query /var/lib/cwl/stga7a84ea3-3799-4c30-9a98-8978fff492d8/GCF_003097635.1_ASM309763v1_genomic.fna.gz --refList GCF_003097635.1_ASM309763v1_genomic.fna/target_genomes.txt --output GCF_003097635.1_ASM309763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:49,659] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:49,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg382225d0-6f1e-4c4f-97d7-c8d2811ee515/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:49,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg382225d0-6f1e-4c4f-97d7-c8d2811ee515/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:49,679] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:49,679] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:49,680] [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 psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	100.0	1051	1055	95	conclusive
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.4557	395	1055	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	79.3254	487	1055	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	79.1259	385	1055	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	79.0973	380	1055	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	78.9178	391	1055	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	78.8942	354	1055	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	78.6605	334	1055	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.5571	330	1055	95	below_threshold
Flavobacterium hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	78.3265	265	1055	95	below_threshold
Flavobacterium hydatis	strain=ATCC 29551	GCA_002217335.1	991	991	type	True	78.2279	262	1055	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	78.2074	283	1055	95	below_threshold
Flavobacterium turcicum	strain=F-339	GCA_011365745.1	2764718	2764718	type	True	78.1084	256	1055	95	below_threshold
Flavobacterium psychrophilum	strain=ATCC 49418	GCA_002217405.1	96345	96345	type	True	78.0547	210	1055	95	below_threshold
Flavobacterium psychrophilum	strain=DSM 3660	GCA_900101925.1	96345	96345	type	True	78.0333	208	1055	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	78.0074	263	1055	95	below_threshold
Flavobacterium tiangeerense	strain=CGMCC 1.6847	GCA_007830355.1	459471	459471	type	True	78.0066	260	1055	95	below_threshold
Flavobacterium psychrophilum	strain=FPG3	GCA_000754405.1	96345	96345	type	True	77.9942	217	1055	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.9805	255	1055	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	77.8783	254	1055	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	77.8767	251	1055	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	77.8226	248	1055	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.8197	224	1055	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.7533	246	1055	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.0956	156	1055	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.0698	156	1055	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:49,681] [INFO] DFAST Taxonomy check result was written to GCF_003097635.1_ASM309763v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:49,682] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:49,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:49,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg382225d0-6f1e-4c4f-97d7-c8d2811ee515/dqc_reference/checkm_data
[2024-01-24 14:06:49,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:49,718] [INFO] Task started: CheckM
[2024-01-24 14:06:49,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003097635.1_ASM309763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003097635.1_ASM309763v1_genomic.fna/checkm_input GCF_003097635.1_ASM309763v1_genomic.fna/checkm_result
[2024-01-24 14:07:31,082] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:31,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:31,102] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:31,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:31,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003097635.1_ASM309763v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:31,103] [INFO] Task started: Blastn
[2024-01-24 14:07:31,104] [INFO] Running command: blastn -query GCF_003097635.1_ASM309763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg382225d0-6f1e-4c4f-97d7-c8d2811ee515/dqc_reference/reference_markers_gtdb.fasta -out GCF_003097635.1_ASM309763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:32,044] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:32,048] [INFO] Selected 23 target genomes.
[2024-01-24 14:07:32,048] [INFO] Target genome list was writen to GCF_003097635.1_ASM309763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:32,067] [INFO] Task started: fastANI
[2024-01-24 14:07:32,068] [INFO] Running command: fastANI --query /var/lib/cwl/stga7a84ea3-3799-4c30-9a98-8978fff492d8/GCF_003097635.1_ASM309763v1_genomic.fna.gz --refList GCF_003097635.1_ASM309763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003097635.1_ASM309763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:47,329] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:47,358] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:47,359] [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_003097635.1	s__Flavobacterium psychrotolerans	100.0	1051	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007097265.1	s__Flavobacterium gawalongense	79.456	395	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_008806775.1	s__Flavobacterium luteum	79.3254	487	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277675.1	s__Flavobacterium soyangense	79.1571	371	1055	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	79.1556	382	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_002413745.1	s__Flavobacterium sp002413745	79.0782	373	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCF_002754315.1	s__Flavobacterium sp002754315	79.0279	402	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_002920895.1	s__Flavobacterium alvei	78.8942	354	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379405.1	s__Flavobacterium sp014379405	78.8898	315	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718345.1	s__Flavobacterium sp016718345	78.7666	391	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003968755.1	s__Flavobacterium sp003968755	78.6373	317	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.86	96.58	0.85	0.82	9	-
GCA_903837025.1	s__Flavobacterium sp903837025	78.5386	228	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823965.1	s__Flavobacterium sp013823965	78.4493	344	1055	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	78.372	297	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737695.1	s__Flavobacterium hydatis	78.3252	264	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_900106645.1	s__Flavobacterium degerlachei	78.22	282	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422725.1	s__Flavobacterium sp001422725	78.1176	266	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839195.1	s__Flavobacterium sp903839195	78.0801	234	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
GCF_002217405.1	s__Flavobacterium psychrophilum	78.0547	210	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.22	98.91	0.92	0.83	157	-
GCF_004797125.1	s__Flavobacterium sangjuense	77.7533	246	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525665.1	s__Flavobacterium sp003525665	77.5112	234	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	77.385	235	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	77.3767	213	1055	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 14:07:47,361] [INFO] GTDB search result was written to GCF_003097635.1_ASM309763v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:47,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:47,375] [INFO] DFAST_QC result json was written to GCF_003097635.1_ASM309763v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:47,375] [INFO] DFAST_QC completed!
[2024-01-24 14:07:47,375] [INFO] Total running time: 0h1m33s