[2024-01-24 14:06:06,924] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,926] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1fe4c22-2d35-4177-b61a-d71166178972/dqc_reference
[2024-01-24 14:06:08,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,359] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,360] [INFO] Running command: gunzip -c /var/lib/cwl/stg0786b5f8-07ad-4ac9-9693-0071de53df9e/GCF_007830155.1_ASM783015v1_genomic.fna.gz | prodigal -d GCF_007830155.1_ASM783015v1_genomic.fna/cds.fna -a GCF_007830155.1_ASM783015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:22,250] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:22,251] [INFO] Task started: HMMsearch
[2024-01-24 14:06:22,251] [INFO] Running command: hmmsearch --tblout GCF_007830155.1_ASM783015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1fe4c22-2d35-4177-b61a-d71166178972/dqc_reference/reference_markers.hmm GCF_007830155.1_ASM783015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:22,608] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:22,609] [INFO] Found 6/6 markers.
[2024-01-24 14:06:22,662] [INFO] Query marker FASTA was written to GCF_007830155.1_ASM783015v1_genomic.fna/markers.fasta
[2024-01-24 14:06:22,662] [INFO] Task started: Blastn
[2024-01-24 14:06:22,662] [INFO] Running command: blastn -query GCF_007830155.1_ASM783015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1fe4c22-2d35-4177-b61a-d71166178972/dqc_reference/reference_markers.fasta -out GCF_007830155.1_ASM783015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:23,516] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:23,519] [INFO] Selected 22 target genomes.
[2024-01-24 14:06:23,520] [INFO] Target genome list was writen to GCF_007830155.1_ASM783015v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:23,529] [INFO] Task started: fastANI
[2024-01-24 14:06:23,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg0786b5f8-07ad-4ac9-9693-0071de53df9e/GCF_007830155.1_ASM783015v1_genomic.fna.gz --refList GCF_007830155.1_ASM783015v1_genomic.fna/target_genomes.txt --output GCF_007830155.1_ASM783015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:42,561] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:42,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1fe4c22-2d35-4177-b61a-d71166178972/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:42,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1fe4c22-2d35-4177-b61a-d71166178972/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:42,580] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:42,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:42,581] [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 duriflava	strain=CGMCC 1.6858	GCA_007830155.1	459528	459528	type	True	100.0	1624	1626	95	conclusive
Pseudomonas zeshuii	strain=KACC 15471	GCA_900141925.1	1076620	1076620	type	True	79.9434	648	1626	95	below_threshold
Pseudomonas asuensis	strain=JCM 13501	GCA_014646755.1	1825787	1825787	type	True	79.5886	552	1626	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	77.6731	193	1626	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	77.6099	194	1626	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	77.5346	274	1626	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	77.5324	181	1626	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.5165	144	1626	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	77.4836	280	1626	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	77.4057	201	1626	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	77.3718	202	1626	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	77.3716	193	1626	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	77.2682	183	1626	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	77.2603	170	1626	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	77.216	183	1626	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	77.1739	199	1626	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	77.1327	201	1626	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	77.0671	175	1626	95	below_threshold
Thiopseudomonas denitrificans	strain=DSM 28679	GCA_004363035.1	1501432	1501432	type	True	76.7873	65	1626	95	below_threshold
Thiopseudomonas denitrificans	strain=X2	GCA_002866065.1	1501432	1501432	type	True	76.7752	66	1626	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	76.7657	193	1626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:42,584] [INFO] DFAST Taxonomy check result was written to GCF_007830155.1_ASM783015v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:42,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:42,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:42,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1fe4c22-2d35-4177-b61a-d71166178972/dqc_reference/checkm_data
[2024-01-24 14:06:42,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:42,640] [INFO] Task started: CheckM
[2024-01-24 14:06:42,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830155.1_ASM783015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830155.1_ASM783015v1_genomic.fna/checkm_input GCF_007830155.1_ASM783015v1_genomic.fna/checkm_result
[2024-01-24 14:07:25,519] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:25,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:25,544] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:25,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:25,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830155.1_ASM783015v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:25,545] [INFO] Task started: Blastn
[2024-01-24 14:07:25,545] [INFO] Running command: blastn -query GCF_007830155.1_ASM783015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1fe4c22-2d35-4177-b61a-d71166178972/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830155.1_ASM783015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:26,792] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:26,795] [INFO] Selected 17 target genomes.
[2024-01-24 14:07:26,795] [INFO] Target genome list was writen to GCF_007830155.1_ASM783015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:26,810] [INFO] Task started: fastANI
[2024-01-24 14:07:26,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg0786b5f8-07ad-4ac9-9693-0071de53df9e/GCF_007830155.1_ASM783015v1_genomic.fna.gz --refList GCF_007830155.1_ASM783015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830155.1_ASM783015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:41,653] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:41,667] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:41,667] [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_007830155.1	s__Pseudomonas_B duriflava	100.0	1624	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002091675.1	s__Pseudomonas_B luteola	79.6141	584	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.05	97.34	0.90	0.85	19	-
GCF_014646755.1	s__Pseudomonas_B asuensis	79.5702	554	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	77.8615	240	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCF_001518815.1	s__Pseudomonas_B oryzihabitans_E	77.7617	254	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.13	98.08	0.95	0.93	4	-
GCF_001512295.1	s__Pseudomonas_B sp001512295	77.6234	278	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	77.6099	194	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
GCF_900099785.1	s__Pseudomonas panipatensis	77.3906	202	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877905.1	s__Pseudomonas nicosulfuronedens	77.3812	200	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007665395.1	s__Pseudomonas_B psychrotolerans_C	77.2831	272	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	77.2681	171	1626	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_009789555.1	s__Pseudomonas_A stutzeri_R	77.2407	176	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.81	99.81	0.96	0.96	2	-
GCF_900106015.1	s__Pseudomonas_E sihuiensis	77.196	201	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_002197815.1	s__Pseudomonas_E oleovorans	77.1321	202	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	97.92	96.68	0.87	0.80	18	-
GCF_009363155.1	s__Azotobacter salinestris	77.0456	167	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015471405.1	s__Pseudomonas_E cichorii_D	76.96	196	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.41	0.90	0.90	2	-
GCF_002866065.1	s__Thiopseudomonas denitrificans	76.8061	67	1626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Thiopseudomonas	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:41,669] [INFO] GTDB search result was written to GCF_007830155.1_ASM783015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:41,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:41,674] [INFO] DFAST_QC result json was written to GCF_007830155.1_ASM783015v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:41,674] [INFO] DFAST_QC completed!
[2024-01-24 14:07:41,674] [INFO] Total running time: 0h1m35s