[2024-01-24 13:57:14,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:14,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:14,267] [INFO] DQC Reference Directory: /var/lib/cwl/stgac662135-9e61-4cac-b6a4-f02558e9a3fe/dqc_reference
[2024-01-24 13:57:15,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:15,697] [INFO] Task started: Prodigal
[2024-01-24 13:57:15,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d2d8cf4-26db-4675-ac37-b0584899a998/GCF_001043005.1_G8688_genomic.fna.gz | prodigal -d GCF_001043005.1_G8688_genomic.fna/cds.fna -a GCF_001043005.1_G8688_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:33,867] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:33,868] [INFO] Task started: HMMsearch
[2024-01-24 13:57:33,868] [INFO] Running command: hmmsearch --tblout GCF_001043005.1_G8688_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac662135-9e61-4cac-b6a4-f02558e9a3fe/dqc_reference/reference_markers.hmm GCF_001043005.1_G8688_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:34,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:34,197] [INFO] Found 6/6 markers.
[2024-01-24 13:57:34,250] [INFO] Query marker FASTA was written to GCF_001043005.1_G8688_genomic.fna/markers.fasta
[2024-01-24 13:57:34,251] [INFO] Task started: Blastn
[2024-01-24 13:57:34,251] [INFO] Running command: blastn -query GCF_001043005.1_G8688_genomic.fna/markers.fasta -db /var/lib/cwl/stgac662135-9e61-4cac-b6a4-f02558e9a3fe/dqc_reference/reference_markers.fasta -out GCF_001043005.1_G8688_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:35,116] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:35,120] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:35,121] [INFO] Target genome list was writen to GCF_001043005.1_G8688_genomic.fna/target_genomes.txt
[2024-01-24 13:57:35,127] [INFO] Task started: fastANI
[2024-01-24 13:57:35,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d2d8cf4-26db-4675-ac37-b0584899a998/GCF_001043005.1_G8688_genomic.fna.gz --refList GCF_001043005.1_G8688_genomic.fna/target_genomes.txt --output GCF_001043005.1_G8688_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:52,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:52,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac662135-9e61-4cac-b6a4-f02558e9a3fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:52,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac662135-9e61-4cac-b6a4-f02558e9a3fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:52,882] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:52,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:52,882] [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 psychrophila	strain=DSM 17535	GCA_001043005.1	122355	122355	type	True	100.0	1743	1743	95	conclusive
Pseudomonas psychrophila	strain=CCUG 53877	GCA_008801485.1	122355	122355	type	True	99.9974	1736	1743	95	conclusive
Pseudomonas deceptionensis	strain=DSM 26521	GCA_001042895.1	882211	882211	type	True	89.1522	1391	1743	95	below_threshold
Pseudomonas deceptionensis	strain=LMG 25555	GCA_900106095.1	882211	882211	type	True	89.1053	1406	1743	95	below_threshold
Pseudomonas fragi	strain=NBRC 3458	GCA_002091615.1	296	296	type	True	87.5684	1308	1743	95	below_threshold
Pseudomonas fragi	strain=NRRL B-727	GCA_900105835.1	296	296	type	True	87.5424	1349	1743	95	below_threshold
Pseudomonas taetrolens	strain=NCTC10697	GCA_900475285.1	47884	47884	type	True	84.9319	1144	1743	95	below_threshold
Pseudomonas taetrolens	strain=DSM 21104	GCA_001042915.1	47884	47884	type	True	84.8903	1153	1743	95	below_threshold
Pseudomonas helleri	strain=DSM 29165	GCA_001043025.1	1608996	1608996	type	True	84.3343	1138	1743	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.3983	914	1743	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	81.2689	899	1743	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	79.8365	647	1743	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	79.8067	626	1743	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	79.5331	739	1743	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:52,888] [INFO] DFAST Taxonomy check result was written to GCF_001043005.1_G8688_genomic.fna/tc_result.tsv
[2024-01-24 13:57:52,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:52,890] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:52,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac662135-9e61-4cac-b6a4-f02558e9a3fe/dqc_reference/checkm_data
[2024-01-24 13:57:52,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:52,945] [INFO] Task started: CheckM
[2024-01-24 13:57:52,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001043005.1_G8688_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001043005.1_G8688_genomic.fna/checkm_input GCF_001043005.1_G8688_genomic.fna/checkm_result
[2024-01-24 13:58:46,381] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:46,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:46,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:46,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:46,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001043005.1_G8688_genomic.fna/markers.fasta)
[2024-01-24 13:58:46,407] [INFO] Task started: Blastn
[2024-01-24 13:58:46,407] [INFO] Running command: blastn -query GCF_001043005.1_G8688_genomic.fna/markers.fasta -db /var/lib/cwl/stgac662135-9e61-4cac-b6a4-f02558e9a3fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_001043005.1_G8688_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:47,703] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:47,706] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:47,706] [INFO] Target genome list was writen to GCF_001043005.1_G8688_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:47,716] [INFO] Task started: fastANI
[2024-01-24 13:58:47,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d2d8cf4-26db-4675-ac37-b0584899a998/GCF_001043005.1_G8688_genomic.fna.gz --refList GCF_001043005.1_G8688_genomic.fna/target_genomes_gtdb.txt --output GCF_001043005.1_G8688_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:01,342] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:01,359] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:01,359] [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_001043005.1	s__Pseudomonas_E psychrophila	100.0	1743	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.62	99.23	0.96	0.92	7	conclusive
GCF_900106095.1	s__Pseudomonas_E deceptionensis	89.1015	1406	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002269505.1	s__Pseudomonas_E fragi_D	87.7907	1312	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.09	96.09	0.88	0.88	2	-
GCF_900618535.1	s__Pseudomonas_E bubulae	87.542	1332	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.96	0.92	0.87	18	-
GCF_900105835.1	s__Pseudomonas_E fragi	87.5332	1350	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.76	96.96	0.94	0.89	28	-
GCF_904063065.1	s__Pseudomonas_E paraversuta	85.6074	1222	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.22	0.95	0.95	9	-
GCF_900475285.1	s__Pseudomonas_E taetrolens	84.9302	1143	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.98	0.99	0.99	4	-
GCF_001043025.1	s__Pseudomonas_E helleri	84.3318	1138	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.29	96.40	0.86	0.80	22	-
GCF_001043055.1	s__Pseudomonas_E weihenstephanensis	84.2655	1050	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.02	97.13	0.92	0.88	6	-
GCF_001411475.1	s__Pseudomonas_E endophytica	82.8041	977	1743	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_001945365.1	s__Pseudomonas_E reinekei	81.563	893	1743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	95.43	0.93	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:01,360] [INFO] GTDB search result was written to GCF_001043005.1_G8688_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:01,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:01,364] [INFO] DFAST_QC result json was written to GCF_001043005.1_G8688_genomic.fna/dqc_result.json
[2024-01-24 13:59:01,365] [INFO] DFAST_QC completed!
[2024-01-24 13:59:01,365] [INFO] Total running time: 0h1m47s