[2024-01-24 13:01:39,639] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,642] [INFO] DQC Reference Directory: /var/lib/cwl/stgd49d3f63-2f5b-4777-b3aa-bf6599fd63be/dqc_reference
[2024-01-24 13:01:41,315] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,316] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,316] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8e53318-b38d-4695-97b6-e4c3ae27b549/GCF_003576595.1_ASM357659v1_genomic.fna.gz | prodigal -d GCF_003576595.1_ASM357659v1_genomic.fna/cds.fna -a GCF_003576595.1_ASM357659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:51,854] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:51,855] [INFO] Task started: HMMsearch
[2024-01-24 13:01:51,855] [INFO] Running command: hmmsearch --tblout GCF_003576595.1_ASM357659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd49d3f63-2f5b-4777-b3aa-bf6599fd63be/dqc_reference/reference_markers.hmm GCF_003576595.1_ASM357659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:52,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:52,167] [INFO] Found 6/6 markers.
[2024-01-24 13:01:52,203] [INFO] Query marker FASTA was written to GCF_003576595.1_ASM357659v1_genomic.fna/markers.fasta
[2024-01-24 13:01:52,204] [INFO] Task started: Blastn
[2024-01-24 13:01:52,204] [INFO] Running command: blastn -query GCF_003576595.1_ASM357659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd49d3f63-2f5b-4777-b3aa-bf6599fd63be/dqc_reference/reference_markers.fasta -out GCF_003576595.1_ASM357659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:52,996] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:52,999] [INFO] Selected 21 target genomes.
[2024-01-24 13:01:53,000] [INFO] Target genome list was writen to GCF_003576595.1_ASM357659v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:53,009] [INFO] Task started: fastANI
[2024-01-24 13:01:53,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8e53318-b38d-4695-97b6-e4c3ae27b549/GCF_003576595.1_ASM357659v1_genomic.fna.gz --refList GCF_003576595.1_ASM357659v1_genomic.fna/target_genomes.txt --output GCF_003576595.1_ASM357659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:08,271] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:08,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd49d3f63-2f5b-4777-b3aa-bf6599fd63be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:08,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd49d3f63-2f5b-4777-b3aa-bf6599fd63be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:08,283] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:08,283] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:08,283] [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
Pusillimonas maritima	strain=17-4A	GCA_003576595.1	2026239	2026239	type	True	100.0	1071	1073	95	conclusive
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.8486	251	1073	95	below_threshold
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	77.6002	121	1073	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	77.4889	123	1073	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	77.1983	107	1073	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	77.0968	124	1073	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	77.0666	92	1073	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	76.6047	95	1073	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	76.5599	91	1073	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	76.514	99	1073	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	76.3506	93	1073	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	76.2643	97	1073	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:08,285] [INFO] DFAST Taxonomy check result was written to GCF_003576595.1_ASM357659v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:08,285] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:08,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:08,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd49d3f63-2f5b-4777-b3aa-bf6599fd63be/dqc_reference/checkm_data
[2024-01-24 13:02:08,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:08,320] [INFO] Task started: CheckM
[2024-01-24 13:02:08,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003576595.1_ASM357659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003576595.1_ASM357659v1_genomic.fna/checkm_input GCF_003576595.1_ASM357659v1_genomic.fna/checkm_result
[2024-01-24 13:02:43,744] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:43,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:43,770] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:43,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:43,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003576595.1_ASM357659v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:43,771] [INFO] Task started: Blastn
[2024-01-24 13:02:43,772] [INFO] Running command: blastn -query GCF_003576595.1_ASM357659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd49d3f63-2f5b-4777-b3aa-bf6599fd63be/dqc_reference/reference_markers_gtdb.fasta -out GCF_003576595.1_ASM357659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:45,102] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:45,105] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:45,105] [INFO] Target genome list was writen to GCF_003576595.1_ASM357659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:45,120] [INFO] Task started: fastANI
[2024-01-24 13:02:45,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8e53318-b38d-4695-97b6-e4c3ae27b549/GCF_003576595.1_ASM357659v1_genomic.fna.gz --refList GCF_003576595.1_ASM357659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003576595.1_ASM357659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:53,678] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:53,693] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:53,693] [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_003576595.1	s__Pusillimonas_A maritima	100.0	1071	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	96.55	95.88	0.88	0.85	8	conclusive
GCF_011388195.1	s__Pusillimonas_A sp011388195	94.7845	933	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694155.1	s__Pusillimonas_A sp002694155	84.6979	349	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384935.1	s__Pusillimonas_A sp002384935	83.8516	766	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.90	98.23	0.90	0.79	9	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	77.8909	227	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCF_014237865.1	s__Pusillimonas_A sp014237865	77.8486	251	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849615.1	s__Candidimonas_A sp002849615	77.3689	96	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022565.1	s__Pusillimonas_D thiosulfatoxidans	77.3188	108	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_D	95.0	97.98	97.65	0.84	0.81	3	-
GCF_002209565.1	s__Candidimonas nitroreducens	77.0968	124	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218885.1	s__Bordetella_A sp019218885	76.6988	102	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:53,695] [INFO] GTDB search result was written to GCF_003576595.1_ASM357659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:53,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:53,703] [INFO] DFAST_QC result json was written to GCF_003576595.1_ASM357659v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:53,703] [INFO] DFAST_QC completed!
[2024-01-24 13:02:53,704] [INFO] Total running time: 0h1m14s