[2024-01-24 15:14:52,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:52,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:52,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg30f5b523-ae38-4626-b8a7-bb3cb5dc3a95/dqc_reference
[2024-01-24 15:14:53,356] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,357] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg04365254-d631-4469-af60-af7c738b6b99/GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/cds.fna -a GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:12,406] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:12,407] [INFO] Task started: HMMsearch
[2024-01-24 15:15:12,407] [INFO] Running command: hmmsearch --tblout GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30f5b523-ae38-4626-b8a7-bb3cb5dc3a95/dqc_reference/reference_markers.hmm GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:12,745] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:12,746] [INFO] Found 6/6 markers.
[2024-01-24 15:15:12,801] [INFO] Query marker FASTA was written to GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:15:12,802] [INFO] Task started: Blastn
[2024-01-24 15:15:12,802] [INFO] Running command: blastn -query GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg30f5b523-ae38-4626-b8a7-bb3cb5dc3a95/dqc_reference/reference_markers.fasta -out GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:13,767] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:13,771] [INFO] Selected 10 target genomes.
[2024-01-24 15:15:13,772] [INFO] Target genome list was writen to GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:15:13,777] [INFO] Task started: fastANI
[2024-01-24 15:15:13,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg04365254-d631-4469-af60-af7c738b6b99/GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna.gz --refList GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:27,302] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:27,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30f5b523-ae38-4626-b8a7-bb3cb5dc3a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:27,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30f5b523-ae38-4626-b8a7-bb3cb5dc3a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:27,312] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:15:27,312] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:15:27,312] [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 viridiflava	strain=ICMP2848	GCA_001401215.1	33069	33069	type	True	87.6664	1463	2038	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	87.6423	1457	2038	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	87.6323	1453	2038	95	below_threshold
Pseudomonas viridiflava	strain=ICMP 2848	GCA_001642795.1	33069	33069	type	True	87.6009	1554	2038	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	87.6005	1448	2038	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	83.9394	1331	2038	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	83.5867	1344	2038	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	83.4731	1343	2038	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	80.1315	727	2038	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	79.9714	775	2038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:27,316] [INFO] DFAST Taxonomy check result was written to GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:15:27,317] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:27,317] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:27,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30f5b523-ae38-4626-b8a7-bb3cb5dc3a95/dqc_reference/checkm_data
[2024-01-24 15:15:27,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:27,378] [INFO] Task started: CheckM
[2024-01-24 15:15:27,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/checkm_input GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:16:22,559] [INFO] Task succeeded: CheckM
[2024-01-24 15:16:22,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:16:22,581] [INFO] ===== Completeness check finished =====
[2024-01-24 15:16:22,581] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:16:22,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:16:22,582] [INFO] Task started: Blastn
[2024-01-24 15:16:22,582] [INFO] Running command: blastn -query GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg30f5b523-ae38-4626-b8a7-bb3cb5dc3a95/dqc_reference/reference_markers_gtdb.fasta -out GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:16:24,239] [INFO] Task succeeded: Blastn
[2024-01-24 15:16:24,243] [INFO] Selected 10 target genomes.
[2024-01-24 15:16:24,244] [INFO] Target genome list was writen to GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:16:24,257] [INFO] Task started: fastANI
[2024-01-24 15:16:24,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg04365254-d631-4469-af60-af7c738b6b99/GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna.gz --refList GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:39,109] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:39,118] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:39,118] [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_900143095.1	s__Pseudomonas_E asturiensis	100.0	2037	2038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.96	0.95	0.95	2	conclusive
GCF_014358015.1	s__Pseudomonas_E triticumensis	94.7378	1675	2038	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_001642795.1	s__Pseudomonas_E viridiflava	87.5939	1555	2038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	96.41	0.93	0.89	1379	-
GCF_002723575.1	s__Pseudomonas_E viridiflava_B	87.5058	1548	2038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.78	98.76	0.95	0.94	5	-
GCF_003702045.1	s__Pseudomonas_E viridiflava_C	86.6563	1471	2038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.39	99.39	0.95	0.95	2	-
GCF_002087235.1	s__Pseudomonas_E floridensis	86.3761	1442	2038	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_900103225.1	s__Pseudomonas_E congelans	83.9998	1346	2038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.60	98.04	0.95	0.92	20	-
GCF_001293775.1	s__Pseudomonas_E syringae_P	83.9627	1337	2038	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_000507185.2	s__Pseudomonas_E syringae	83.9162	1370	2038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	97.83	96.00	0.92	0.85	147	-
GCF_900100365.1	s__Pseudomonas_E cannabina	83.8235	1349	2038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.50	95.44	0.90	0.84	17	-
--------------------------------------------------------------------------------
[2024-01-24 15:16:39,120] [INFO] GTDB search result was written to GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:39,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:39,124] [INFO] DFAST_QC result json was written to GCF_900143095.1_IMG-taxon_2663762795_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:16:39,124] [INFO] DFAST_QC completed!
[2024-01-24 15:16:39,124] [INFO] Total running time: 0h1m47s