[2024-01-24 12:13:28,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,845] [INFO] DQC Reference Directory: /var/lib/cwl/stgc279253a-92cb-496d-bd3f-8fc179a19b82/dqc_reference
[2024-01-24 12:13:30,304] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,305] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,305] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdcce5b4-56bc-491b-b1c9-32514a67e4e8/GCF_002091635.1_ASM209163v1_genomic.fna.gz | prodigal -d GCF_002091635.1_ASM209163v1_genomic.fna/cds.fna -a GCF_002091635.1_ASM209163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:50,481] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:50,481] [INFO] Task started: HMMsearch
[2024-01-24 12:13:50,481] [INFO] Running command: hmmsearch --tblout GCF_002091635.1_ASM209163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc279253a-92cb-496d-bd3f-8fc179a19b82/dqc_reference/reference_markers.hmm GCF_002091635.1_ASM209163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:50,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:50,876] [INFO] Found 6/6 markers.
[2024-01-24 12:13:50,939] [INFO] Query marker FASTA was written to GCF_002091635.1_ASM209163v1_genomic.fna/markers.fasta
[2024-01-24 12:13:50,940] [INFO] Task started: Blastn
[2024-01-24 12:13:50,940] [INFO] Running command: blastn -query GCF_002091635.1_ASM209163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc279253a-92cb-496d-bd3f-8fc179a19b82/dqc_reference/reference_markers.fasta -out GCF_002091635.1_ASM209163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:52,072] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:52,077] [INFO] Selected 28 target genomes.
[2024-01-24 12:13:52,077] [INFO] Target genome list was writen to GCF_002091635.1_ASM209163v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:52,089] [INFO] Task started: fastANI
[2024-01-24 12:13:52,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdcce5b4-56bc-491b-b1c9-32514a67e4e8/GCF_002091635.1_ASM209163v1_genomic.fna.gz --refList GCF_002091635.1_ASM209163v1_genomic.fna/target_genomes.txt --output GCF_002091635.1_ASM209163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:22,263] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:22,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc279253a-92cb-496d-bd3f-8fc179a19b82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:22,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc279253a-92cb-496d-bd3f-8fc179a19b82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:22,293] [INFO] Found 28 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:22,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:22,294] [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 indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	100.0	1900	1901	95	conclusive
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	99.9781	1881	1901	95	conclusive
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	82.9953	1002	1901	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	82.5233	960	1901	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.4513	945	1901	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	82.3936	952	1901	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	82.3751	956	1901	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.3689	1074	1901	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	82.3247	1107	1901	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	82.2629	838	1901	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	82.2224	1053	1901	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	82.1921	866	1901	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.9918	954	1901	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	81.9685	894	1901	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	81.7928	877	1901	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	81.5619	982	1901	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	81.3723	833	1901	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.36	819	1901	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	81.3226	742	1901	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	81.2712	746	1901	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	81.2446	823	1901	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	81.2132	813	1901	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	81.1547	822	1901	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	81.0853	777	1901	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	80.9959	828	1901	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	80.8912	800	1901	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	80.5475	762	1901	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	80.5117	739	1901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:22,295] [INFO] DFAST Taxonomy check result was written to GCF_002091635.1_ASM209163v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:22,296] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:22,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:22,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc279253a-92cb-496d-bd3f-8fc179a19b82/dqc_reference/checkm_data
[2024-01-24 12:14:22,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:22,353] [INFO] Task started: CheckM
[2024-01-24 12:14:22,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002091635.1_ASM209163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002091635.1_ASM209163v1_genomic.fna/checkm_input GCF_002091635.1_ASM209163v1_genomic.fna/checkm_result
[2024-01-24 12:15:17,797] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:17,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:17,821] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:17,821] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:17,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002091635.1_ASM209163v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:17,822] [INFO] Task started: Blastn
[2024-01-24 12:15:17,822] [INFO] Running command: blastn -query GCF_002091635.1_ASM209163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc279253a-92cb-496d-bd3f-8fc179a19b82/dqc_reference/reference_markers_gtdb.fasta -out GCF_002091635.1_ASM209163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,987] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,991] [INFO] Selected 25 target genomes.
[2024-01-24 12:15:19,991] [INFO] Target genome list was writen to GCF_002091635.1_ASM209163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:20,008] [INFO] Task started: fastANI
[2024-01-24 12:15:20,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdcce5b4-56bc-491b-b1c9-32514a67e4e8/GCF_002091635.1_ASM209163v1_genomic.fna.gz --refList GCF_002091635.1_ASM209163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002091635.1_ASM209163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:48,455] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:48,482] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:48,483] [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_002091635.1	s__Pseudomonas_M indica	100.0	1900	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	conclusive
GCF_002286785.1	s__Pseudomonas_M sp002286785	94.5143	1644	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	83.0189	999	1901	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_009799925.1	s__Pseudomonas_E sp009799925	82.9583	961	1901	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_000474255.1	s__Pseudomonas_F alcaligenes_A	82.648	1082	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.08	97.69	0.89	0.89	3	-
GCF_000412695.1	s__Pseudomonas_F resinovorans_A	82.6092	1040	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	82.5973	1079	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_005508865.1	s__Pseudomonas_E sp005508865	82.4355	980	1901	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_002890915.1	s__Pseudomonas_A stutzeri_AF	82.3144	878	1901	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_000761545.1	s__Pseudomonas_E sp000761545	82.2731	928	1901	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_004521985.1	s__Pseudomonas_E khazarica	82.2232	988	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCF_014851565.1	s__Pseudomonas_E sp014851565	82.2016	982	1901	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_900104265.1	s__Pseudomonas_E guguanensis	82.1933	1058	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	97.13	0.85	0.85	2	-
GCF_013200955.2	s__Pseudomonas_E campi	82.1806	868	1901	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_014851905.1	s__Pseudomonas_E sp014851905	82.0266	898	1901	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	81.9919	954	1901	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_900106975.1	s__Pseudomonas_O kuykendallii	81.968	895	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	96.83	96.68	0.93	0.91	4	-
GCF_008041835.1	s__Pseudomonas_E sp002282595	81.7834	828	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_005844005.1	s__Pseudomonas_A sp000765155	81.4746	820	1901	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_000219605.1	s__Pseudomonas_A stutzeri	81.3734	818	1901	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_000380335.1	s__Azotobacter vinelandii	81.3372	743	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
GCF_000802425.1	s__Pseudomonas_H flexibilis	81.3126	743	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	99.07	98.74	0.94	0.90	5	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	81.2081	835	1901	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_000495915.1	s__Pseudomonas_A chloritidismutans	81.0894	777	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCF_003586265.1	s__Pseudomonas_D jilinensis	78.9253	376	1901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.07	95.47	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:48,485] [INFO] GTDB search result was written to GCF_002091635.1_ASM209163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:48,485] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:48,494] [INFO] DFAST_QC result json was written to GCF_002091635.1_ASM209163v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:48,494] [INFO] DFAST_QC completed!
[2024-01-24 12:15:48,495] [INFO] Total running time: 0h2m20s