[2024-01-25 19:30:21,557] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:30:21,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:30:21,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg09d450dc-5d2f-4528-8319-83a65db972c9/dqc_reference
[2024-01-25 19:30:22,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:30:22,679] [INFO] Task started: Prodigal
[2024-01-25 19:30:22,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg3162e6c0-dba2-4f94-b528-bb76e3ccca87/GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna.gz | prodigal -d GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/cds.fna -a GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:30:32,661] [INFO] Task succeeded: Prodigal
[2024-01-25 19:30:32,661] [INFO] Task started: HMMsearch
[2024-01-25 19:30:32,661] [INFO] Running command: hmmsearch --tblout GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09d450dc-5d2f-4528-8319-83a65db972c9/dqc_reference/reference_markers.hmm GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:30:32,872] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:30:32,874] [INFO] Found 6/6 markers.
[2024-01-25 19:30:32,905] [INFO] Query marker FASTA was written to GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/markers.fasta
[2024-01-25 19:30:32,905] [INFO] Task started: Blastn
[2024-01-25 19:30:32,905] [INFO] Running command: blastn -query GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/markers.fasta -db /var/lib/cwl/stg09d450dc-5d2f-4528-8319-83a65db972c9/dqc_reference/reference_markers.fasta -out GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:30:33,640] [INFO] Task succeeded: Blastn
[2024-01-25 19:30:33,643] [INFO] Selected 17 target genomes.
[2024-01-25 19:30:33,643] [INFO] Target genome list was writen to GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/target_genomes.txt
[2024-01-25 19:30:33,653] [INFO] Task started: fastANI
[2024-01-25 19:30:33,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg3162e6c0-dba2-4f94-b528-bb76e3ccca87/GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna.gz --refList GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/target_genomes.txt --output GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:30:46,851] [INFO] Task succeeded: fastANI
[2024-01-25 19:30:46,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09d450dc-5d2f-4528-8319-83a65db972c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:30:46,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09d450dc-5d2f-4528-8319-83a65db972c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:30:46,863] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:30:46,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:30:46,863] [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 nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	100.0	1285	1287	95	conclusive
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	81.6203	780	1287	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.0835	574	1287	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.874	606	1287	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.8394	555	1287	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	79.7307	501	1287	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	79.6936	587	1287	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	79.6822	581	1287	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.5701	499	1287	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	79.5515	497	1287	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.497	527	1287	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.493	567	1287	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.0332	464	1287	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	79.0098	366	1287	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.7084	299	1287	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	78.6638	419	1287	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	78.3714	364	1287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:30:46,864] [INFO] DFAST Taxonomy check result was written to GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/tc_result.tsv
[2024-01-25 19:30:46,865] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:30:46,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:30:46,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09d450dc-5d2f-4528-8319-83a65db972c9/dqc_reference/checkm_data
[2024-01-25 19:30:46,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:30:46,905] [INFO] Task started: CheckM
[2024-01-25 19:30:46,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/checkm_input GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/checkm_result
[2024-01-25 19:31:18,669] [INFO] Task succeeded: CheckM
[2024-01-25 19:31:18,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:31:18,691] [INFO] ===== Completeness check finished =====
[2024-01-25 19:31:18,691] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:31:18,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/markers.fasta)
[2024-01-25 19:31:18,693] [INFO] Task started: Blastn
[2024-01-25 19:31:18,693] [INFO] Running command: blastn -query GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/markers.fasta -db /var/lib/cwl/stg09d450dc-5d2f-4528-8319-83a65db972c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:31:19,987] [INFO] Task succeeded: Blastn
[2024-01-25 19:31:19,990] [INFO] Selected 17 target genomes.
[2024-01-25 19:31:19,990] [INFO] Target genome list was writen to GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:31:20,005] [INFO] Task started: fastANI
[2024-01-25 19:31:20,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg3162e6c0-dba2-4f94-b528-bb76e3ccca87/GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna.gz --refList GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/target_genomes_gtdb.txt --output GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:31:33,463] [INFO] Task succeeded: fastANI
[2024-01-25 19:31:33,474] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:31:33,474] [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_000708045.1	s__Marinobacter nitratireducens	100.0	1285	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.86	98.83	0.90	0.89	3	conclusive
GCF_008370345.1	s__Marinobacter sp008370345	81.6164	780	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	80.0766	575	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	79.9007	463	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	79.8429	555	1287	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	79.7423	580	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCF_000347775.1	s__Marinobacter santoriniensis	79.7307	501	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933295.1	s__Marinobacter flavimaris	79.6717	583	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	79.6598	577	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.5753	498	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_001045555.1	s__Marinobacter subterrani	79.4929	590	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_003994855.1	s__Marinobacter sp003994855	79.4626	504	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	79.4193	408	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	79.3761	513	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	79.3497	496	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301335.1	s__Marinobacter sp017301335	79.1246	424	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007675.1	s__Marinobacter fuscus	78.6638	419	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:31:33,477] [INFO] GTDB search result was written to GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/result_gtdb.tsv
[2024-01-25 19:31:33,478] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:31:33,482] [INFO] DFAST_QC result json was written to GCF_000708045.1_Marinobacter_sp._AK21_genomic.fna/dqc_result.json
[2024-01-25 19:31:33,483] [INFO] DFAST_QC completed!
[2024-01-25 19:31:33,483] [INFO] Total running time: 0h1m12s