[2024-01-24 12:39:40,292] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:40,294] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:40,294] [INFO] DQC Reference Directory: /var/lib/cwl/stge5abd515-94fe-4cfc-91f3-a9573e420db9/dqc_reference
[2024-01-24 12:39:41,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:41,676] [INFO] Task started: Prodigal
[2024-01-24 12:39:41,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg067cc7a4-cfed-4f24-a112-e3b3547f6fdd/GCF_003052585.1_ASM305258v1_genomic.fna.gz | prodigal -d GCF_003052585.1_ASM305258v1_genomic.fna/cds.fna -a GCF_003052585.1_ASM305258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:54,153] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:54,153] [INFO] Task started: HMMsearch
[2024-01-24 12:39:54,153] [INFO] Running command: hmmsearch --tblout GCF_003052585.1_ASM305258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5abd515-94fe-4cfc-91f3-a9573e420db9/dqc_reference/reference_markers.hmm GCF_003052585.1_ASM305258v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:54,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:54,484] [INFO] Found 6/6 markers.
[2024-01-24 12:39:54,525] [INFO] Query marker FASTA was written to GCF_003052585.1_ASM305258v1_genomic.fna/markers.fasta
[2024-01-24 12:39:54,526] [INFO] Task started: Blastn
[2024-01-24 12:39:54,526] [INFO] Running command: blastn -query GCF_003052585.1_ASM305258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5abd515-94fe-4cfc-91f3-a9573e420db9/dqc_reference/reference_markers.fasta -out GCF_003052585.1_ASM305258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:55,693] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:55,697] [INFO] Selected 28 target genomes.
[2024-01-24 12:39:55,697] [INFO] Target genome list was writen to GCF_003052585.1_ASM305258v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:55,706] [INFO] Task started: fastANI
[2024-01-24 12:39:55,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg067cc7a4-cfed-4f24-a112-e3b3547f6fdd/GCF_003052585.1_ASM305258v1_genomic.fna.gz --refList GCF_003052585.1_ASM305258v1_genomic.fna/target_genomes.txt --output GCF_003052585.1_ASM305258v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:24,125] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:24,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5abd515-94fe-4cfc-91f3-a9573e420db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:24,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5abd515-94fe-4cfc-91f3-a9573e420db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:24,159] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:24,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:24,160] [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
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	100.0	1335	1339	95	conclusive
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.2304	754	1339	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	82.2004	793	1339	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	82.1741	640	1339	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	82.1263	781	1339	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	81.9855	656	1339	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.9853	613	1339	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.9054	781	1339	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	81.7934	747	1339	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	81.6142	753	1339	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.5976	733	1339	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	81.568	720	1339	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	81.4874	759	1339	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	81.4775	747	1339	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	81.444	613	1339	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	81.4393	747	1339	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	81.2612	596	1339	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.2509	681	1339	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	81.2124	773	1339	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	81.2049	778	1339	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	81.1941	666	1339	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	81.1056	721	1339	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	81.0774	717	1339	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	81.0745	677	1339	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	81.0564	704	1339	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	81.0383	693	1339	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	80.8107	628	1339	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	80.6963	631	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:24,162] [INFO] DFAST Taxonomy check result was written to GCF_003052585.1_ASM305258v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:24,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:24,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:24,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5abd515-94fe-4cfc-91f3-a9573e420db9/dqc_reference/checkm_data
[2024-01-24 12:40:24,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:24,209] [INFO] Task started: CheckM
[2024-01-24 12:40:24,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003052585.1_ASM305258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003052585.1_ASM305258v1_genomic.fna/checkm_input GCF_003052585.1_ASM305258v1_genomic.fna/checkm_result
[2024-01-24 12:41:02,025] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:02,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:02,051] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:02,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:02,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003052585.1_ASM305258v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:02,053] [INFO] Task started: Blastn
[2024-01-24 12:41:02,053] [INFO] Running command: blastn -query GCF_003052585.1_ASM305258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5abd515-94fe-4cfc-91f3-a9573e420db9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003052585.1_ASM305258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:04,098] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:04,101] [INFO] Selected 25 target genomes.
[2024-01-24 12:41:04,102] [INFO] Target genome list was writen to GCF_003052585.1_ASM305258v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:04,138] [INFO] Task started: fastANI
[2024-01-24 12:41:04,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg067cc7a4-cfed-4f24-a112-e3b3547f6fdd/GCF_003052585.1_ASM305258v1_genomic.fna.gz --refList GCF_003052585.1_ASM305258v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003052585.1_ASM305258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:27,202] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:27,225] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:27,225] [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_003052585.1	s__Pseudomonas_E mangrovi	100.0	1334	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009799925.1	s__Pseudomonas_E sp009799925	82.6123	759	1339	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_003205495.1	s__Pseudomonas_E alcaligenes_B	82.4796	777	1339	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_003696305.1	s__Pseudomonas_E sp003696305	82.2874	784	1339	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_000467105.1	s__Pseudomonas_E alcaligenes	82.2528	770	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	82.1975	761	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_005508865.1	s__Pseudomonas_E sp005508865	82.193	792	1339	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_900115715.1	s__Pseudomonas_K sagittaria	82.1712	643	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	82.1322	593	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_900156545.1	s__Pseudomonas_E alcaligenes_A	82.0625	746	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCF_019097855.1	s__Pseudomonas_K sp019097855	82.0313	609	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	81.9768	658	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761545.1	s__Pseudomonas_E sp000761545	81.8088	741	1339	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_900109175.1	s__Pseudomonas_K linyingensis	81.8004	645	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592875.1	s__Pseudomonas_E sp001592875	81.6367	751	1339	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_016901015.1	s__Pseudomonas_E sp016901015	81.6207	730	1339	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_014174475.1	s__Pseudomonas_E sp014174475	81.5347	724	1339	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_900187975.1	s__Pseudomonas delhiensis	81.4883	759	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_003052605.1	s__Pseudomonas_E indoloxydans	81.3017	693	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	N/A	N/A	N/A	N/A	1	-
GCF_005876855.1	s__Pseudomonas_R nosocomialis	81.0449	693	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCF_013522825.1	s__Pseudomonas_A stutzeri_AK	80.9032	620	1339	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_900188455.1	s__Pseudomonas_E japonica	80.7009	630	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013522725.1	s__Pseudomonas_R azotifigens_A	80.3863	637	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766265.1	s__Pseudomonas_R sp900766265	80.3033	615	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331645.1	s__Pseudomonas_A stutzeri_T	80.0934	548	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.46	98.46	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:27,226] [INFO] GTDB search result was written to GCF_003052585.1_ASM305258v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:27,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:27,232] [INFO] DFAST_QC result json was written to GCF_003052585.1_ASM305258v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:27,232] [INFO] DFAST_QC completed!
[2024-01-24 12:41:27,232] [INFO] Total running time: 0h1m47s