[2024-01-24 14:11:51,562] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:51,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:51,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg806a720d-f392-48d9-9f46-6ca163c4596c/dqc_reference
[2024-01-24 14:11:53,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:53,045] [INFO] Task started: Prodigal
[2024-01-24 14:11:53,046] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1b22b9e-3326-47ca-ae92-8206093d5222/GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/cds.fna -a GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:06,842] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:06,842] [INFO] Task started: HMMsearch
[2024-01-24 14:12:06,842] [INFO] Running command: hmmsearch --tblout GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg806a720d-f392-48d9-9f46-6ca163c4596c/dqc_reference/reference_markers.hmm GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:07,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:07,217] [INFO] Found 6/6 markers.
[2024-01-24 14:12:07,275] [INFO] Query marker FASTA was written to GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:07,281] [INFO] Task started: Blastn
[2024-01-24 14:12:07,281] [INFO] Running command: blastn -query GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg806a720d-f392-48d9-9f46-6ca163c4596c/dqc_reference/reference_markers.fasta -out GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:08,336] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:08,339] [INFO] Selected 15 target genomes.
[2024-01-24 14:12:08,340] [INFO] Target genome list was writen to GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:08,344] [INFO] Task started: fastANI
[2024-01-24 14:12:08,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1b22b9e-3326-47ca-ae92-8206093d5222/GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna.gz --refList GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:24,002] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:24,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg806a720d-f392-48d9-9f46-6ca163c4596c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:24,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg806a720d-f392-48d9-9f46-6ca163c4596c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:24,042] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:12:24,042] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:24,042] [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
Stutzerimonas balearica	strain=DSM 6083	GCA_900103375.1	74829	74829	type	True	100.0	1439	1441	95	conclusive
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	99.9945	1436	1441	95	conclusive
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	84.3084	1053	1441	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	84.2498	1072	1441	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	84.1892	1000	1441	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	84.1748	1005	1441	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	84.162	1016	1441	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	84.1607	1040	1441	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	84.1603	1010	1441	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	84.1141	1017	1441	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	83.4208	960	1441	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	83.3821	973	1441	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	81.2775	742	1441	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	80.9057	668	1441	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.8983	679	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:24,044] [INFO] DFAST Taxonomy check result was written to GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:12:24,045] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:24,045] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:24,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg806a720d-f392-48d9-9f46-6ca163c4596c/dqc_reference/checkm_data
[2024-01-24 14:12:24,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:24,121] [INFO] Task started: CheckM
[2024-01-24 14:12:24,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/checkm_input GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:07,608] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:07,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:07,633] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:07,633] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:07,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:07,634] [INFO] Task started: Blastn
[2024-01-24 14:13:07,634] [INFO] Running command: blastn -query GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg806a720d-f392-48d9-9f46-6ca163c4596c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:09,561] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:09,565] [INFO] Selected 15 target genomes.
[2024-01-24 14:13:09,565] [INFO] Target genome list was writen to GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:09,581] [INFO] Task started: fastANI
[2024-01-24 14:13:09,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1b22b9e-3326-47ca-ae92-8206093d5222/GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna.gz --refList GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:24,798] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:24,862] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:24,863] [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_000818015.1	s__Pseudomonas_A balearica	99.9945	1436	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.54	98.20	0.91	0.86	18	conclusive
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	84.4159	1039	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	84.2675	1067	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	84.1455	1029	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	84.0678	967	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005844005.1	s__Pseudomonas_A sp000765155	83.9907	984	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.19	98.01	0.92	0.89	5	-
GCF_907163115.1	s__Pseudomonas_A stutzeri_AL	83.8764	997	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	83.7632	1000	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	83.5289	999	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	83.3947	963	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	83.2588	931	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	82.4547	894	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	81.2639	743	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	80.9015	679	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003595175.1	s__Pseudomonas_E sp003595175	80.8692	680	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:24,864] [INFO] GTDB search result was written to GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:24,865] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:24,880] [INFO] DFAST_QC result json was written to GCF_900103375.1_IMG-taxon_2602042028_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:24,880] [INFO] DFAST_QC completed!
[2024-01-24 14:13:24,881] [INFO] Total running time: 0h1m33s