[2024-01-24 14:30:59,347] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,349] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,349] [INFO] DQC Reference Directory: /var/lib/cwl/stga1d67e5a-fea7-4bdd-985a-026064a09a58/dqc_reference
[2024-01-24 14:31:00,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,556] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg3293b2c6-fd72-4c65-ac39-da3ec0580230/GCF_000730645.1_ASM73064v1_genomic.fna.gz | prodigal -d GCF_000730645.1_ASM73064v1_genomic.fna/cds.fna -a GCF_000730645.1_ASM73064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:16,970] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:16,970] [INFO] Task started: HMMsearch
[2024-01-24 14:31:16,970] [INFO] Running command: hmmsearch --tblout GCF_000730645.1_ASM73064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1d67e5a-fea7-4bdd-985a-026064a09a58/dqc_reference/reference_markers.hmm GCF_000730645.1_ASM73064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:17,289] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:17,291] [INFO] Found 6/6 markers.
[2024-01-24 14:31:17,352] [INFO] Query marker FASTA was written to GCF_000730645.1_ASM73064v1_genomic.fna/markers.fasta
[2024-01-24 14:31:17,352] [INFO] Task started: Blastn
[2024-01-24 14:31:17,352] [INFO] Running command: blastn -query GCF_000730645.1_ASM73064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1d67e5a-fea7-4bdd-985a-026064a09a58/dqc_reference/reference_markers.fasta -out GCF_000730645.1_ASM73064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:18,391] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:18,395] [INFO] Selected 19 target genomes.
[2024-01-24 14:31:18,395] [INFO] Target genome list was writen to GCF_000730645.1_ASM73064v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:18,403] [INFO] Task started: fastANI
[2024-01-24 14:31:18,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg3293b2c6-fd72-4c65-ac39-da3ec0580230/GCF_000730645.1_ASM73064v1_genomic.fna.gz --refList GCF_000730645.1_ASM73064v1_genomic.fna/target_genomes.txt --output GCF_000730645.1_ASM73064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:41,167] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:41,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1d67e5a-fea7-4bdd-985a-026064a09a58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:41,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1d67e5a-fea7-4bdd-985a-026064a09a58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:41,186] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:41,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:41,187] [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 parafulva	strain=NBRC 16636	GCA_000730645.1	157782	157782	suspected-type	True	100.0	1621	1623	95	conclusive
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	99.9958	1612	1623	95	conclusive
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	86.043	1243	1623	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	85.9581	1200	1623	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	85.9245	1254	1623	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	85.9107	1257	1623	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	85.8962	1201	1623	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	85.8794	1246	1623	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	85.8747	1225	1623	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	85.8378	1268	1623	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	85.8232	1116	1623	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	85.7578	1205	1623	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	85.7139	1195	1623	95	below_threshold
Pseudomonas juntendi	strain=BML3	GCA_009932375.1	2666183	2666183	type	True	85.2892	1140	1623	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	85.1091	1195	1623	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	85.0828	1151	1623	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	84.6266	1142	1623	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	84.5941	1163	1623	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	84.5916	1146	1623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:41,193] [INFO] DFAST Taxonomy check result was written to GCF_000730645.1_ASM73064v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:41,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:41,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:41,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1d67e5a-fea7-4bdd-985a-026064a09a58/dqc_reference/checkm_data
[2024-01-24 14:31:41,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:41,248] [INFO] Task started: CheckM
[2024-01-24 14:31:41,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000730645.1_ASM73064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000730645.1_ASM73064v1_genomic.fna/checkm_input GCF_000730645.1_ASM73064v1_genomic.fna/checkm_result
[2024-01-24 14:32:30,485] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:30,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:30,511] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:30,511] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:30,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000730645.1_ASM73064v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:30,512] [INFO] Task started: Blastn
[2024-01-24 14:32:30,512] [INFO] Running command: blastn -query GCF_000730645.1_ASM73064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1d67e5a-fea7-4bdd-985a-026064a09a58/dqc_reference/reference_markers_gtdb.fasta -out GCF_000730645.1_ASM73064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:32,436] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:32,439] [INFO] Selected 22 target genomes.
[2024-01-24 14:32:32,440] [INFO] Target genome list was writen to GCF_000730645.1_ASM73064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:32,461] [INFO] Task started: fastANI
[2024-01-24 14:32:32,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg3293b2c6-fd72-4c65-ac39-da3ec0580230/GCF_000730645.1_ASM73064v1_genomic.fna.gz --refList GCF_000730645.1_ASM73064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000730645.1_ASM73064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:00,503] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:00,527] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:00,527] [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_000730645.1	s__Pseudomonas_E parafulva	100.0	1621	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.15	97.35	0.92	0.90	6	conclusive
GCF_001642705.1	s__Pseudomonas_E sp001642705	86.4112	1225	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	86.2828	1197	1623	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_003331055.1	s__Pseudomonas_E sp003331055	86.2024	1162	1623	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_009932335.1	s__Pseudomonas_E asiatica	86.1605	1239	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	86.1154	1184	1623	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_002113165.1	s__Pseudomonas_E sp002113165	86.0707	1212	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900277125.1	s__Pseudomonas_E inefficax	86.0578	1241	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCF_015680405.1	s__Pseudomonas_E pudica	86.0001	1206	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_012975065.1	s__Pseudomonas_E sp012975065	85.9936	1213	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.74	0.94	0.94	3	-
GCF_000708715.2	s__Pseudomonas_E putida_R	85.955	1256	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.68	95.68	0.85	0.85	2	-
GCF_000412675.1	s__Pseudomonas_E putida	85.9198	1256	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	97.45	0.89	0.83	24	-
GCF_000730605.1	s__Pseudomonas_E monteilii	85.8896	1203	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	-
GCF_013393325.1	s__Pseudomonas_E putida_P	85.7987	1251	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	99.27	0.91	0.82	10	-
GCF_013373935.1	s__Pseudomonas_E sp002438125	85.7964	1119	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_003627215.1	s__Pseudomonas_E sp001422615	85.5745	1192	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009391885.1	s__Pseudomonas_E sp009391885	85.3355	1183	1623	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_009932375.1	s__Pseudomonas_E juntendi	85.3039	1138	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	84.9755	1142	1623	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_003205295.1	s__Pseudomonas_E mosselii_B	84.8113	1141	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_016861355.1	s__Pseudomonas_E sp001259595	84.7909	1156	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	95.65	95.59	0.90	0.88	5	-
GCF_000621225.1	s__Pseudomonas_E mosselii	84.5844	1147	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:00,529] [INFO] GTDB search result was written to GCF_000730645.1_ASM73064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:00,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:00,538] [INFO] DFAST_QC result json was written to GCF_000730645.1_ASM73064v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:00,538] [INFO] DFAST_QC completed!
[2024-01-24 14:33:00,538] [INFO] Total running time: 0h2m1s