[2024-01-24 12:37:08,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:08,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:08,367] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8dfe229-a930-4a21-bc9c-0b85f1067fc5/dqc_reference
[2024-01-24 12:37:09,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:09,699] [INFO] Task started: Prodigal
[2024-01-24 12:37:09,699] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0d628ce-7d8a-45a3-bf2e-4fb963a54a9d/GCF_018728565.1_ASM1872856v1_genomic.fna.gz | prodigal -d GCF_018728565.1_ASM1872856v1_genomic.fna/cds.fna -a GCF_018728565.1_ASM1872856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:29,744] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:29,745] [INFO] Task started: HMMsearch
[2024-01-24 12:37:29,745] [INFO] Running command: hmmsearch --tblout GCF_018728565.1_ASM1872856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8dfe229-a930-4a21-bc9c-0b85f1067fc5/dqc_reference/reference_markers.hmm GCF_018728565.1_ASM1872856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:30,050] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:30,051] [INFO] Found 6/6 markers.
[2024-01-24 12:37:30,096] [INFO] Query marker FASTA was written to GCF_018728565.1_ASM1872856v1_genomic.fna/markers.fasta
[2024-01-24 12:37:30,097] [INFO] Task started: Blastn
[2024-01-24 12:37:30,097] [INFO] Running command: blastn -query GCF_018728565.1_ASM1872856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8dfe229-a930-4a21-bc9c-0b85f1067fc5/dqc_reference/reference_markers.fasta -out GCF_018728565.1_ASM1872856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:30,764] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:30,768] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:30,769] [INFO] Target genome list was writen to GCF_018728565.1_ASM1872856v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:30,780] [INFO] Task started: fastANI
[2024-01-24 12:37:30,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0d628ce-7d8a-45a3-bf2e-4fb963a54a9d/GCF_018728565.1_ASM1872856v1_genomic.fna.gz --refList GCF_018728565.1_ASM1872856v1_genomic.fna/target_genomes.txt --output GCF_018728565.1_ASM1872856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:42,357] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:42,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8dfe229-a930-4a21-bc9c-0b85f1067fc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:42,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8dfe229-a930-4a21-bc9c-0b85f1067fc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:42,369] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:42,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:42,369] [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
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	100.0	1625	1625	95	conclusive
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	85.133	1220	1625	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	82.0962	1077	1625	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	81.7923	1003	1625	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	81.3994	973	1625	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	81.3568	831	1625	95	below_threshold
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	81.1959	963	1625	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	80.664	848	1625	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.4964	85	1625	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.4491	67	1625	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.4385	56	1625	95	below_threshold
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	76.3492	110	1625	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	76.3166	110	1625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:42,371] [INFO] DFAST Taxonomy check result was written to GCF_018728565.1_ASM1872856v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:42,372] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:42,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:42,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8dfe229-a930-4a21-bc9c-0b85f1067fc5/dqc_reference/checkm_data
[2024-01-24 12:37:42,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:42,423] [INFO] Task started: CheckM
[2024-01-24 12:37:42,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018728565.1_ASM1872856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018728565.1_ASM1872856v1_genomic.fna/checkm_input GCF_018728565.1_ASM1872856v1_genomic.fna/checkm_result
[2024-01-24 12:38:38,639] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:38,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:38,664] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:38,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:38,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018728565.1_ASM1872856v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:38,665] [INFO] Task started: Blastn
[2024-01-24 12:38:38,665] [INFO] Running command: blastn -query GCF_018728565.1_ASM1872856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8dfe229-a930-4a21-bc9c-0b85f1067fc5/dqc_reference/reference_markers_gtdb.fasta -out GCF_018728565.1_ASM1872856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:39,486] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:39,494] [INFO] Selected 11 target genomes.
[2024-01-24 12:38:39,494] [INFO] Target genome list was writen to GCF_018728565.1_ASM1872856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:39,506] [INFO] Task started: fastANI
[2024-01-24 12:38:39,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0d628ce-7d8a-45a3-bf2e-4fb963a54a9d/GCF_018728565.1_ASM1872856v1_genomic.fna.gz --refList GCF_018728565.1_ASM1872856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018728565.1_ASM1872856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:51,493] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:51,509] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:51,510] [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_018728565.1	s__Zobellia russellii	100.0	1625	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	conclusive
GCF_009725985.1	s__Zobellia amurskyensis	85.133	1220	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_015330165.1	s__Zobellia sp015330165	82.1011	1076	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_009725995.1	s__Zobellia laminariae	81.7974	1002	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603515.1	s__Zobellia sp018603515	81.3994	973	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156625.1	s__Zobellia uliginosa	81.357	831	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330125.1	s__Zobellia sp015330125	81.1959	963	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCF_018860745.1	s__Zobellia uliginosa_B	80.9206	928	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	80.6641	848	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_014349235.1	s__Euzebyella sp014349235	77.4765	263	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235875.1	s__Croceivirga lutea	76.3492	110	1625	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:51,511] [INFO] GTDB search result was written to GCF_018728565.1_ASM1872856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:51,512] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:51,515] [INFO] DFAST_QC result json was written to GCF_018728565.1_ASM1872856v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:51,515] [INFO] DFAST_QC completed!
[2024-01-24 12:38:51,515] [INFO] Total running time: 0h1m43s