[2024-01-24 12:06:13,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg74c5b692-5d97-4b7c-a5c7-a1a09df91bb9/dqc_reference
[2024-01-24 12:06:14,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,692] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fc6a118-e9c3-4b19-bd41-2a242a90aca5/GCF_000243115.2_ASM24311v3_genomic.fna.gz | prodigal -d GCF_000243115.2_ASM24311v3_genomic.fna/cds.fna -a GCF_000243115.2_ASM24311v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:38,257] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:38,257] [INFO] Task started: HMMsearch
[2024-01-24 12:06:38,257] [INFO] Running command: hmmsearch --tblout GCF_000243115.2_ASM24311v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74c5b692-5d97-4b7c-a5c7-a1a09df91bb9/dqc_reference/reference_markers.hmm GCF_000243115.2_ASM24311v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:38,630] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:38,632] [INFO] Found 6/6 markers.
[2024-01-24 12:06:38,674] [INFO] Query marker FASTA was written to GCF_000243115.2_ASM24311v3_genomic.fna/markers.fasta
[2024-01-24 12:06:38,675] [INFO] Task started: Blastn
[2024-01-24 12:06:38,675] [INFO] Running command: blastn -query GCF_000243115.2_ASM24311v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg74c5b692-5d97-4b7c-a5c7-a1a09df91bb9/dqc_reference/reference_markers.fasta -out GCF_000243115.2_ASM24311v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:39,282] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:39,286] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:39,286] [INFO] Target genome list was writen to GCF_000243115.2_ASM24311v3_genomic.fna/target_genomes.txt
[2024-01-24 12:06:39,297] [INFO] Task started: fastANI
[2024-01-24 12:06:39,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc6a118-e9c3-4b19-bd41-2a242a90aca5/GCF_000243115.2_ASM24311v3_genomic.fna.gz --refList GCF_000243115.2_ASM24311v3_genomic.fna/target_genomes.txt --output GCF_000243115.2_ASM24311v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:57,565] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:57,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74c5b692-5d97-4b7c-a5c7-a1a09df91bb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:57,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74c5b692-5d97-4b7c-a5c7-a1a09df91bb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:57,579] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:57,579] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:57,579] [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
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	100.0	1565	1565	95	conclusive
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	78.3254	437	1565	95	below_threshold
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	78.1441	562	1565	95	below_threshold
Niabella aurantiaca	strain=DSM 17617	GCA_000374125.1	379900	379900	type	True	78.0993	442	1565	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	77.6991	473	1565	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	77.539	475	1565	95	below_threshold
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	76.7317	76	1565	95	below_threshold
Niabella yanshanensis	strain=HAMBI_3031	GCA_003349965.1	577386	577386	type	True	76.6509	132	1565	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.3266	91	1565	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.2507	57	1565	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	75.8959	60	1565	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.8878	87	1565	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	75.8572	73	1565	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	75.8074	90	1565	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	75.6421	74	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:57,581] [INFO] DFAST Taxonomy check result was written to GCF_000243115.2_ASM24311v3_genomic.fna/tc_result.tsv
[2024-01-24 12:06:57,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:57,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:57,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74c5b692-5d97-4b7c-a5c7-a1a09df91bb9/dqc_reference/checkm_data
[2024-01-24 12:06:57,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:57,628] [INFO] Task started: CheckM
[2024-01-24 12:06:57,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000243115.2_ASM24311v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000243115.2_ASM24311v3_genomic.fna/checkm_input GCF_000243115.2_ASM24311v3_genomic.fna/checkm_result
[2024-01-24 12:08:00,217] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:00,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:00,242] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:00,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:00,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000243115.2_ASM24311v3_genomic.fna/markers.fasta)
[2024-01-24 12:08:00,243] [INFO] Task started: Blastn
[2024-01-24 12:08:00,243] [INFO] Running command: blastn -query GCF_000243115.2_ASM24311v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg74c5b692-5d97-4b7c-a5c7-a1a09df91bb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000243115.2_ASM24311v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:01,151] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:01,156] [INFO] Selected 15 target genomes.
[2024-01-24 12:08:01,156] [INFO] Target genome list was writen to GCF_000243115.2_ASM24311v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:01,170] [INFO] Task started: fastANI
[2024-01-24 12:08:01,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc6a118-e9c3-4b19-bd41-2a242a90aca5/GCF_000243115.2_ASM24311v3_genomic.fna.gz --refList GCF_000243115.2_ASM24311v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000243115.2_ASM24311v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:14,652] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:14,670] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:14,670] [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_000243115.2	s__Niabella soli	100.0	1565	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017744795.1	s__Niabella sp017744795	84.962	1075	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101395.1	s__Niabella drilacis	78.3168	438	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654455.1	s__Niabella ginsenosidivorans	78.091	559	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374125.1	s__Niabella aurantiaca	78.0555	443	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744715.1	s__Niabella sp017744715	77.7445	463	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001896965.1	s__Niabella sp001896965	76.8088	84	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708305.1	s__Niabella sp016708305	76.4918	75	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399735.1	s__Terrimonas sp002399735	76.4359	65	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	76.2345	90	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002352145.1	s__JJ008 sp002352145	76.216	50	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898485.1	s__46-32 sp001898485	76.0343	79	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	99.14	98.30	0.96	0.92	3	-
GCA_004173355.1	s__46-32 sp004173355	75.8599	66	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	75.6421	74	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:14,672] [INFO] GTDB search result was written to GCF_000243115.2_ASM24311v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:14,673] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:14,676] [INFO] DFAST_QC result json was written to GCF_000243115.2_ASM24311v3_genomic.fna/dqc_result.json
[2024-01-24 12:08:14,676] [INFO] DFAST_QC completed!
[2024-01-24 12:08:14,676] [INFO] Total running time: 0h2m1s