[2024-01-24 14:47:08,435] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg1138bc8f-881f-431b-98bb-507948e3afc1/dqc_reference
[2024-01-24 14:47:09,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,886] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg99777b16-5bd4-45e5-946c-97aa59f104b5/GCF_005871205.1_ASM587120v1_genomic.fna.gz | prodigal -d GCF_005871205.1_ASM587120v1_genomic.fna/cds.fna -a GCF_005871205.1_ASM587120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:23,169] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:23,169] [INFO] Task started: HMMsearch
[2024-01-24 14:47:23,169] [INFO] Running command: hmmsearch --tblout GCF_005871205.1_ASM587120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1138bc8f-881f-431b-98bb-507948e3afc1/dqc_reference/reference_markers.hmm GCF_005871205.1_ASM587120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:23,593] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:23,595] [INFO] Found 6/6 markers.
[2024-01-24 14:47:23,647] [INFO] Query marker FASTA was written to GCF_005871205.1_ASM587120v1_genomic.fna/markers.fasta
[2024-01-24 14:47:23,647] [INFO] Task started: Blastn
[2024-01-24 14:47:23,647] [INFO] Running command: blastn -query GCF_005871205.1_ASM587120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1138bc8f-881f-431b-98bb-507948e3afc1/dqc_reference/reference_markers.fasta -out GCF_005871205.1_ASM587120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:24,515] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:24,519] [INFO] Selected 16 target genomes.
[2024-01-24 14:47:24,520] [INFO] Target genome list was writen to GCF_005871205.1_ASM587120v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:24,526] [INFO] Task started: fastANI
[2024-01-24 14:47:24,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg99777b16-5bd4-45e5-946c-97aa59f104b5/GCF_005871205.1_ASM587120v1_genomic.fna.gz --refList GCF_005871205.1_ASM587120v1_genomic.fna/target_genomes.txt --output GCF_005871205.1_ASM587120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:39,176] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:39,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1138bc8f-881f-431b-98bb-507948e3afc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:39,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1138bc8f-881f-431b-98bb-507948e3afc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:39,190] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:39,190] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:39,190] [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
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	100.0	1437	1438	95	conclusive
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	89.9468	1104	1438	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	89.632	1048	1438	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	81.3211	818	1438	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	80.2828	666	1438	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.2736	613	1438	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	80.1725	693	1438	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	80.1288	664	1438	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	80.0777	687	1438	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.8336	533	1438	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.8057	559	1438	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.7878	541	1438	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	79.6956	549	1438	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	79.4873	413	1438	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	79.3292	529	1438	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.8659	479	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:39,192] [INFO] DFAST Taxonomy check result was written to GCF_005871205.1_ASM587120v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:39,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:39,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:39,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1138bc8f-881f-431b-98bb-507948e3afc1/dqc_reference/checkm_data
[2024-01-24 14:47:39,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:39,235] [INFO] Task started: CheckM
[2024-01-24 14:47:39,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005871205.1_ASM587120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005871205.1_ASM587120v1_genomic.fna/checkm_input GCF_005871205.1_ASM587120v1_genomic.fna/checkm_result
[2024-01-24 14:48:22,113] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:22,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:22,146] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:22,147] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:22,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005871205.1_ASM587120v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:22,148] [INFO] Task started: Blastn
[2024-01-24 14:48:22,148] [INFO] Running command: blastn -query GCF_005871205.1_ASM587120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1138bc8f-881f-431b-98bb-507948e3afc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_005871205.1_ASM587120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:23,630] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:23,634] [INFO] Selected 18 target genomes.
[2024-01-24 14:48:23,634] [INFO] Target genome list was writen to GCF_005871205.1_ASM587120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:23,646] [INFO] Task started: fastANI
[2024-01-24 14:48:23,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg99777b16-5bd4-45e5-946c-97aa59f104b5/GCF_005871205.1_ASM587120v1_genomic.fna.gz --refList GCF_005871205.1_ASM587120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005871205.1_ASM587120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:39,248] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:39,266] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:39,266] [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_005871205.1	s__Marinobacter alexandrii	100.0	1437	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	conclusive
GCA_000830985.1	s__Marinobacter similis	89.9454	1105	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820575.1	s__Marinobacter sediminum	89.6175	1049	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933275.1	s__Marinobacter maroccanus	80.4823	682	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	80.353	705	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.3262	624	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	80.274	667	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_900115175.1	s__Marinobacter gudaonensis	80.2527	657	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617755.1	s__Marinobacter salsuginis	80.1969	656	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	80.1851	656	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	80.1771	586	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045555.1	s__Marinobacter subterrani	80.1747	692	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_002933295.1	s__Marinobacter flavimaris	80.1288	664	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCA_018623515.1	s__Marinobacter sp018623515	80.0366	518	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003030785.1	s__Marinobacter sp003030785	80.0121	406	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.8382	533	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_000397065.2	s__Marinobacter lipolyticus	79.7095	547	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447155.2	s__Marinobacter sp001447155	79.4633	560	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:39,268] [INFO] GTDB search result was written to GCF_005871205.1_ASM587120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:39,268] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:39,272] [INFO] DFAST_QC result json was written to GCF_005871205.1_ASM587120v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:39,272] [INFO] DFAST_QC completed!
[2024-01-24 14:48:39,272] [INFO] Total running time: 0h1m31s