[2024-01-24 11:44:05,463] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf6bf4ba-cecd-41cd-a283-99429e4fca6e/dqc_reference
[2024-01-24 11:44:08,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,837] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg253a7c9f-0110-4530-9191-63f80e6b332d/GCF_003131185.1_ASM313118v1_genomic.fna.gz | prodigal -d GCF_003131185.1_ASM313118v1_genomic.fna/cds.fna -a GCF_003131185.1_ASM313118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:29,512] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:29,512] [INFO] Task started: HMMsearch
[2024-01-24 11:44:29,513] [INFO] Running command: hmmsearch --tblout GCF_003131185.1_ASM313118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf6bf4ba-cecd-41cd-a283-99429e4fca6e/dqc_reference/reference_markers.hmm GCF_003131185.1_ASM313118v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:29,844] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:29,845] [INFO] Found 6/6 markers.
[2024-01-24 11:44:29,897] [INFO] Query marker FASTA was written to GCF_003131185.1_ASM313118v1_genomic.fna/markers.fasta
[2024-01-24 11:44:29,897] [INFO] Task started: Blastn
[2024-01-24 11:44:29,897] [INFO] Running command: blastn -query GCF_003131185.1_ASM313118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf6bf4ba-cecd-41cd-a283-99429e4fca6e/dqc_reference/reference_markers.fasta -out GCF_003131185.1_ASM313118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:30,895] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:30,898] [INFO] Selected 34 target genomes.
[2024-01-24 11:44:30,898] [INFO] Target genome list was writen to GCF_003131185.1_ASM313118v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:30,911] [INFO] Task started: fastANI
[2024-01-24 11:44:30,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg253a7c9f-0110-4530-9191-63f80e6b332d/GCF_003131185.1_ASM313118v1_genomic.fna.gz --refList GCF_003131185.1_ASM313118v1_genomic.fna/target_genomes.txt --output GCF_003131185.1_ASM313118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:06,491] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:06,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf6bf4ba-cecd-41cd-a283-99429e4fca6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:06,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf6bf4ba-cecd-41cd-a283-99429e4fca6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:06,515] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:45:06,515] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:45:06,515] [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 ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	82.2495	1006	2117	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	81.8915	1039	2117	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	81.8522	960	2117	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	81.8514	918	2117	95	below_threshold
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	81.8366	1041	2117	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	81.832	1078	2117	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	81.7936	1008	2117	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	81.7671	1074	2117	95	below_threshold
Pseudomonas cichorii	strain=DSM 50259	GCA_018343775.1	36746	36746	suspected-type	True	81.7316	1077	2117	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000444135.1	46257	46257	type	True	81.6257	961	2117	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	81.6247	960	2117	95	below_threshold
Pseudomonas avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	81.5813	996	2117	95	below_threshold
Pseudomonas syringae	strain=NCPPB 3739	GCA_000233835.2	317	317	pathovar	True	81.5702	938	2117	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	81.5374	1063	2117	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	81.5322	981	2117	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	81.5309	1015	2117	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	81.5247	980	2117	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	81.5143	1062	2117	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=CFBP 1702	GCA_000935765.1	251701	251701	pathovar	True	81.4885	1056	2117	95	below_threshold
Pseudomonas brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	81.4428	1005	2117	95	below_threshold
Pseudomonas cannabina	strain=ICMP 15200	GCA_001401375.1	86840	86840	pathovar	True	81.4359	967	2117	95	below_threshold
Pseudomonas brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	81.4169	1003	2117	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	81.3843	984	2117	95	below_threshold
Pseudomonas mediterranea	strain=DSM 16733	GCA_900106005.1	183795	183795	type	True	81.372	927	2117	95	below_threshold
Pseudomonas mediterranea	strain=CFBP 5447	GCA_000774145.1	183795	183795	type	True	81.3167	932	2117	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	81.1716	916	2117	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	81.1016	941	2117	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_001401315.1	251699	251699	pathovar	True	81.0409	988	2117	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	81.03	906	2117	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	76.7781	126	2117	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	76.7274	131	2117	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	75.8118	68	2117	95	below_threshold
Exilibacterium tricleocarpae	strain=R142	GCA_007004655.1	2591008	2591008	type	True	75.674	99	2117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:06,517] [INFO] DFAST Taxonomy check result was written to GCF_003131185.1_ASM313118v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:06,517] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:06,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:06,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf6bf4ba-cecd-41cd-a283-99429e4fca6e/dqc_reference/checkm_data
[2024-01-24 11:45:06,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:06,577] [INFO] Task started: CheckM
[2024-01-24 11:45:06,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003131185.1_ASM313118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003131185.1_ASM313118v1_genomic.fna/checkm_input GCF_003131185.1_ASM313118v1_genomic.fna/checkm_result
[2024-01-24 11:46:11,138] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:11,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:11,167] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:11,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:11,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003131185.1_ASM313118v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:11,169] [INFO] Task started: Blastn
[2024-01-24 11:46:11,169] [INFO] Running command: blastn -query GCF_003131185.1_ASM313118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf6bf4ba-cecd-41cd-a283-99429e4fca6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003131185.1_ASM313118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:12,850] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:12,854] [INFO] Selected 21 target genomes.
[2024-01-24 11:46:12,854] [INFO] Target genome list was writen to GCF_003131185.1_ASM313118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:12,870] [INFO] Task started: fastANI
[2024-01-24 11:46:12,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg253a7c9f-0110-4530-9191-63f80e6b332d/GCF_003131185.1_ASM313118v1_genomic.fna.gz --refList GCF_003131185.1_ASM313118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003131185.1_ASM313118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:41,033] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:41,056] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:41,056] [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_003131185.1	s__Pseudomonas_E ovata	100.0	2115	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.40	98.37	0.91	0.91	3	conclusive
GCF_900589395.1	s__Pseudomonas_E sp900589395	93.3547	1830	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.16	0.94	0.93	8	-
GCF_000829415.1	s__Pseudomonas_E sp000829415	83.3436	1368	2117	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_002113595.1	s__Pseudomonas_E sp002113595	82.131	1011	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	96.42	0.97	0.93	16	-
GCF_017165745.1	s__Pseudomonas_E capsici	81.9557	1074	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	97.35	0.95	0.93	13	-
GCF_900497695.1	s__Pseudomonas_E wadenswilerensis	81.83	977	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.26	0.95	0.95	2	-
GCF_900143095.1	s__Pseudomonas_E asturiensis	81.7898	1112	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.96	0.95	0.95	2	-
GCF_014268755.2	s__Pseudomonas_E sp014268755	81.6863	1046	2117	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_000820515.1	s__Pseudomonas_E batumici	81.6859	952	2117	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_001941965.1	s__Pseudomonas_E putida_L	81.6656	1051	2117	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_014358015.1	s__Pseudomonas_E triticumensis	81.6455	1066	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.53	98.52	0.94	0.92	3	-
GCF_000444135.1	s__Pseudomonas_E avellanae	81.6304	960	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.46	0.87	0.79	302	-
GCF_013386115.1	s__Pseudomonas_E gingeri_B	81.6167	1027	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	98.43	0.94	0.92	9	-
GCF_001293775.1	s__Pseudomonas_E syringae_P	81.5752	991	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.87	99.84	0.98	0.97	3	-
GCF_015471405.1	s__Pseudomonas_E cichorii_D	81.5655	1050	2117	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_001466965.1	s__Pseudomonas_E syringae_Q	81.5258	991	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.91	98.87	0.94	0.94	3	-
GCF_000633395.1	s__Pseudomonas_E sp000633395	81.5148	1017	2117	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_000263855.1	s__Pseudomonas_E sp000263855	81.3498	983	2117	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_902498065.1	s__Pseudomonas_E fluorescens_BJ	80.5201	912	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.24	0.94	0.93	3	-
GCF_004803755.1	s__Pseudomonas_E sp004803755	79.9549	724	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	76.1226	216	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:41,058] [INFO] GTDB search result was written to GCF_003131185.1_ASM313118v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:41,059] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:41,064] [INFO] DFAST_QC result json was written to GCF_003131185.1_ASM313118v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:41,064] [INFO] DFAST_QC completed!
[2024-01-24 11:46:41,064] [INFO] Total running time: 0h2m36s