[2024-01-24 12:40:03,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:03,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:03,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c99b57c-17c5-4fba-b5b3-b5b80e74cc5d/dqc_reference
[2024-01-24 12:40:04,864] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:04,865] [INFO] Task started: Prodigal
[2024-01-24 12:40:04,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg97ef1cff-1ca8-41c5-b5f0-85f828e75f92/GCF_011355085.1_ASM1135508v1_genomic.fna.gz | prodigal -d GCF_011355085.1_ASM1135508v1_genomic.fna/cds.fna -a GCF_011355085.1_ASM1135508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:25,153] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:25,154] [INFO] Task started: HMMsearch
[2024-01-24 12:40:25,154] [INFO] Running command: hmmsearch --tblout GCF_011355085.1_ASM1135508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c99b57c-17c5-4fba-b5b3-b5b80e74cc5d/dqc_reference/reference_markers.hmm GCF_011355085.1_ASM1135508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:25,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:25,474] [INFO] Found 6/6 markers.
[2024-01-24 12:40:25,525] [INFO] Query marker FASTA was written to GCF_011355085.1_ASM1135508v1_genomic.fna/markers.fasta
[2024-01-24 12:40:25,526] [INFO] Task started: Blastn
[2024-01-24 12:40:25,526] [INFO] Running command: blastn -query GCF_011355085.1_ASM1135508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c99b57c-17c5-4fba-b5b3-b5b80e74cc5d/dqc_reference/reference_markers.fasta -out GCF_011355085.1_ASM1135508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:26,540] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:26,544] [INFO] Selected 28 target genomes.
[2024-01-24 12:40:26,544] [INFO] Target genome list was writen to GCF_011355085.1_ASM1135508v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:26,561] [INFO] Task started: fastANI
[2024-01-24 12:40:26,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg97ef1cff-1ca8-41c5-b5f0-85f828e75f92/GCF_011355085.1_ASM1135508v1_genomic.fna.gz --refList GCF_011355085.1_ASM1135508v1_genomic.fna/target_genomes.txt --output GCF_011355085.1_ASM1135508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:00,718] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:00,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c99b57c-17c5-4fba-b5b3-b5b80e74cc5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:00,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c99b57c-17c5-4fba-b5b3-b5b80e74cc5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:00,741] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:41:00,741] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:41:00,741] [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 brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.8352	837	2084	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	82.7965	1109	2084	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	82.7927	1099	2084	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	82.7789	1114	2084	95	below_threshold
Pseudomonas chlororaphis subsp. piscium	strain=DSM 21509	GCA_001269555.1	1513890	587753	type	True	82.7241	1120	2084	95	below_threshold
Pseudomonas chlororaphis subsp. piscium	strain=DSM 21509	GCA_003850345.1	1513890	587753	type	True	82.7111	1110	2084	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	82.5477	959	2084	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	82.5195	1089	2084	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	82.3897	1049	2084	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	82.3834	1043	2084	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	82.3782	1051	2084	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	82.2602	1196	2084	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	82.2427	1037	2084	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	82.2338	920	2084	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	82.133	863	2084	95	below_threshold
Pseudomonas umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	82.0465	1136	2084	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	82.0142	1016	2084	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	81.9635	943	2084	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	81.9402	995	2084	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	81.9148	1059	2084	95	below_threshold
Pseudomonas laurentiana	strain=JCM 32154	GCA_014648275.1	2364649	2364649	type	True	81.8416	939	2084	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	81.7518	945	2084	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	81.7359	967	2084	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	81.7283	947	2084	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	81.6382	927	2084	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	81.5562	927	2084	95	below_threshold
Pseudomonas baltica	strain=MBT-2	GCA_014235765.1	2762576	2762576	type	True	81.556	749	2084	95	below_threshold
Pseudomonas coleopterorum	strain=LMG 28558	GCA_900105555.1	1605838	1605838	type	True	81.452	769	2084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:00,743] [INFO] DFAST Taxonomy check result was written to GCF_011355085.1_ASM1135508v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:00,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:00,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:00,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c99b57c-17c5-4fba-b5b3-b5b80e74cc5d/dqc_reference/checkm_data
[2024-01-24 12:41:00,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:00,802] [INFO] Task started: CheckM
[2024-01-24 12:41:00,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011355085.1_ASM1135508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011355085.1_ASM1135508v1_genomic.fna/checkm_input GCF_011355085.1_ASM1135508v1_genomic.fna/checkm_result
[2024-01-24 12:41:58,656] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:58,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:58,679] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:58,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:58,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011355085.1_ASM1135508v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:58,680] [INFO] Task started: Blastn
[2024-01-24 12:41:58,680] [INFO] Running command: blastn -query GCF_011355085.1_ASM1135508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c99b57c-17c5-4fba-b5b3-b5b80e74cc5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_011355085.1_ASM1135508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:00,546] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:00,550] [INFO] Selected 23 target genomes.
[2024-01-24 12:42:00,550] [INFO] Target genome list was writen to GCF_011355085.1_ASM1135508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:00,589] [INFO] Task started: fastANI
[2024-01-24 12:42:00,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg97ef1cff-1ca8-41c5-b5f0-85f828e75f92/GCF_011355085.1_ASM1135508v1_genomic.fna.gz --refList GCF_011355085.1_ASM1135508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011355085.1_ASM1135508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:28,978] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:28,998] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:28,998] [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_011355085.1	s__Pseudomonas_E sp011355085	100.0	2081	2084	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_009905435.1	s__Pseudomonas_E sp009905435	83.2554	1038	2084	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_000259195.1	s__Pseudomonas_E donghuensis	83.0801	1082	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.33	99.30	0.94	0.92	5	-
GCF_018417635.1	s__Pseudomonas_E sp900101695	83.0668	1119	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.49	97.27	0.95	0.94	5	-
GCF_000800615.1	s__Pseudomonas_E putida_F	83.0572	1091	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.83	99.76	0.97	0.96	3	-
GCF_900497695.1	s__Pseudomonas_E wadenswilerensis	83.0557	1127	2084	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_019168305.1	s__Pseudomonas_E sp019168305	82.9594	981	2084	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_002806685.1	s__Pseudomonas_E qingdaonensis	82.9352	1007	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
GCA_010671725.1	s__Pseudomonas_E brassicae	82.8805	833	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.75	0.94	0.94	2	-
GCF_003105155.1	s__Pseudomonas_E sp003105155	82.7882	960	2084	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_003850345.1	s__Pseudomonas_E chlororaphis_F	82.7308	1107	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.16	95.02	0.90	0.86	82	-
GCA_003523465.1	s__Pseudomonas_E sp003523465	82.6853	500	2084	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_013386115.1	s__Pseudomonas_E gingeri_B	82.5478	1045	2084	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_003053605.1	s__Pseudomonas_E sp003053605	82.451	1142	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	-
GCF_003024385.1	s__Pseudomonas_E sp003024385	82.3618	1016	2084	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_902498135.1	s__Pseudomonas_E fluorescens_BH	82.3198	1144	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.39	98.07	0.87	0.86	3	-
GCF_004006335.1	s__Pseudomonas_E sp002112885	82.3131	1030	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_014268755.2	s__Pseudomonas_E sp014268755	82.2309	1031	2084	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_013374995.1	s__Pseudomonas_E eucalypticola	82.2199	922	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	99.03	0.96	0.96	2	-
GCF_014863585.1	s__Pseudomonas_E gozinkensis	82.1341	1063	2084	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_902497875.1	s__Pseudomonas_E fluorescens_BR	82.0746	1107	2084	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_007858285.1	s__Pseudomonas_E brenneri	81.7165	950	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	97.33	0.94	0.88	10	-
GCF_900105555.1	s__Pseudomonas_E coleopterorum	81.4645	767	2084	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.66	96.53	0.90	0.88	9	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:28,999] [INFO] GTDB search result was written to GCF_011355085.1_ASM1135508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:29,000] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:29,006] [INFO] DFAST_QC result json was written to GCF_011355085.1_ASM1135508v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:29,006] [INFO] DFAST_QC completed!
[2024-01-24 12:42:29,006] [INFO] Total running time: 0h2m25s