[2024-01-24 12:57:50,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:50,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:50,174] [INFO] DQC Reference Directory: /var/lib/cwl/stgd634d755-9f4a-4949-95f5-91fe38ad3850/dqc_reference
[2024-01-24 12:57:51,372] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:51,373] [INFO] Task started: Prodigal
[2024-01-24 12:57:51,373] [INFO] Running command: gunzip -c /var/lib/cwl/stgd409fdd2-7b02-4eff-bbfd-d4808f093e25/GCF_025706525.1_ASM2570652v1_genomic.fna.gz | prodigal -d GCF_025706525.1_ASM2570652v1_genomic.fna/cds.fna -a GCF_025706525.1_ASM2570652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:11,132] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:11,133] [INFO] Task started: HMMsearch
[2024-01-24 12:58:11,133] [INFO] Running command: hmmsearch --tblout GCF_025706525.1_ASM2570652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd634d755-9f4a-4949-95f5-91fe38ad3850/dqc_reference/reference_markers.hmm GCF_025706525.1_ASM2570652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:11,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:11,391] [INFO] Found 6/6 markers.
[2024-01-24 12:58:11,438] [INFO] Query marker FASTA was written to GCF_025706525.1_ASM2570652v1_genomic.fna/markers.fasta
[2024-01-24 12:58:11,438] [INFO] Task started: Blastn
[2024-01-24 12:58:11,439] [INFO] Running command: blastn -query GCF_025706525.1_ASM2570652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd634d755-9f4a-4949-95f5-91fe38ad3850/dqc_reference/reference_markers.fasta -out GCF_025706525.1_ASM2570652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:12,355] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:12,358] [INFO] Selected 12 target genomes.
[2024-01-24 12:58:12,358] [INFO] Target genome list was writen to GCF_025706525.1_ASM2570652v1_genomic.fna/target_genomes.txt
[2024-01-24 12:58:12,363] [INFO] Task started: fastANI
[2024-01-24 12:58:12,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgd409fdd2-7b02-4eff-bbfd-d4808f093e25/GCF_025706525.1_ASM2570652v1_genomic.fna.gz --refList GCF_025706525.1_ASM2570652v1_genomic.fna/target_genomes.txt --output GCF_025706525.1_ASM2570652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:32,024] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:32,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd634d755-9f4a-4949-95f5-91fe38ad3850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:32,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd634d755-9f4a-4949-95f5-91fe38ad3850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:32,035] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:58:32,035] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:58:32,035] [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 atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	95.7322	1809	2065	95	inconclusive
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	95.6659	1810	2065	95	inconclusive
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	95.5945	1745	2065	95	inconclusive
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	95.2515	1701	2065	95	inconclusive
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	89.5247	1661	2065	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	88.6811	1665	2065	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.4046	1672	2065	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.0707	1596	2065	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	87.6045	1604	2065	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.4754	1567	2065	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	83.5587	1253	2065	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.9182	856	2065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:32,036] [INFO] DFAST Taxonomy check result was written to GCF_025706525.1_ASM2570652v1_genomic.fna/tc_result.tsv
[2024-01-24 12:58:32,037] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:32,037] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:32,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd634d755-9f4a-4949-95f5-91fe38ad3850/dqc_reference/checkm_data
[2024-01-24 12:58:32,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:32,093] [INFO] Task started: CheckM
[2024-01-24 12:58:32,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025706525.1_ASM2570652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025706525.1_ASM2570652v1_genomic.fna/checkm_input GCF_025706525.1_ASM2570652v1_genomic.fna/checkm_result
[2024-01-24 12:59:30,674] [INFO] Task succeeded: CheckM
[2024-01-24 12:59:30,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:59:30,697] [INFO] ===== Completeness check finished =====
[2024-01-24 12:59:30,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:59:30,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025706525.1_ASM2570652v1_genomic.fna/markers.fasta)
[2024-01-24 12:59:30,698] [INFO] Task started: Blastn
[2024-01-24 12:59:30,698] [INFO] Running command: blastn -query GCF_025706525.1_ASM2570652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd634d755-9f4a-4949-95f5-91fe38ad3850/dqc_reference/reference_markers_gtdb.fasta -out GCF_025706525.1_ASM2570652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:59:32,395] [INFO] Task succeeded: Blastn
[2024-01-24 12:59:32,403] [INFO] Selected 9 target genomes.
[2024-01-24 12:59:32,403] [INFO] Target genome list was writen to GCF_025706525.1_ASM2570652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:59:32,433] [INFO] Task started: fastANI
[2024-01-24 12:59:32,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgd409fdd2-7b02-4eff-bbfd-d4808f093e25/GCF_025706525.1_ASM2570652v1_genomic.fna.gz --refList GCF_025706525.1_ASM2570652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025706525.1_ASM2570652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:59:51,761] [INFO] Task succeeded: fastANI
[2024-01-24 12:59:51,769] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:59:51,770] [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_004801935.1	s__Pseudomonas_E atacamensis	95.7322	1809	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	97.08	95.72	0.92	0.89	59	conclusive
GCF_001605965.1	s__Pseudomonas_E koreensis_C	94.8334	1762	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	98.03	96.36	0.95	0.90	10	-
GCF_000817895.1	s__Pseudomonas_E fluorescens_AO	94.1409	1751	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.16	98.16	0.95	0.95	2	-
GCF_900105805.1	s__Pseudomonas_E moraviensis_A	92.7008	1755	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.30	0.96	0.94	7	-
GCF_002836515.1	s__Pseudomonas_E sp002836515	92.6024	1709	2065	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_014268595.2	s__Pseudomonas_E sp014270125	89.5328	1661	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.59	0.94	0.93	4	-
GCF_900105485.1	s__Pseudomonas_E granadensis	88.6564	1669	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.81	0.93	0.92	8	-
GCF_003999415.1	s__Pseudomonas_E koreensis_E	88.0907	1558	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_016651305.1	s__Pseudomonas_E sp016651305	88.0003	1625	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:59:51,773] [INFO] GTDB search result was written to GCF_025706525.1_ASM2570652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:59:51,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:59:51,777] [INFO] DFAST_QC result json was written to GCF_025706525.1_ASM2570652v1_genomic.fna/dqc_result.json
[2024-01-24 12:59:51,777] [INFO] DFAST_QC completed!
[2024-01-24 12:59:51,777] [INFO] Total running time: 0h2m2s