[2023-06-19 14:28:51,516] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:28:51,521] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:28:51,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg62ef8dbb-32cd-4b30-bafa-0dc89ddcd603/dqc_reference
[2023-06-19 14:28:53,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:28:53,577] [INFO] Task started: Prodigal
[2023-06-19 14:28:53,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg13c9c1e7-4396-4675-89da-902e50632886/GCA_018820925.1_ASM1882092v1_genomic.fna.gz | prodigal -d GCA_018820925.1_ASM1882092v1_genomic.fna/cds.fna -a GCA_018820925.1_ASM1882092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:05,069] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:05,070] [INFO] Task started: HMMsearch
[2023-06-19 14:29:05,070] [INFO] Running command: hmmsearch --tblout GCA_018820925.1_ASM1882092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62ef8dbb-32cd-4b30-bafa-0dc89ddcd603/dqc_reference/reference_markers.hmm GCA_018820925.1_ASM1882092v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:05,352] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:05,355] [INFO] Found 6/6 markers.
[2023-06-19 14:29:05,391] [INFO] Query marker FASTA was written to GCA_018820925.1_ASM1882092v1_genomic.fna/markers.fasta
[2023-06-19 14:29:05,391] [INFO] Task started: Blastn
[2023-06-19 14:29:05,392] [INFO] Running command: blastn -query GCA_018820925.1_ASM1882092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62ef8dbb-32cd-4b30-bafa-0dc89ddcd603/dqc_reference/reference_markers.fasta -out GCA_018820925.1_ASM1882092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:06,327] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:06,332] [INFO] Selected 28 target genomes.
[2023-06-19 14:29:06,333] [INFO] Target genome list was writen to GCA_018820925.1_ASM1882092v1_genomic.fna/target_genomes.txt
[2023-06-19 14:29:06,339] [INFO] Task started: fastANI
[2023-06-19 14:29:06,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c9c1e7-4396-4675-89da-902e50632886/GCA_018820925.1_ASM1882092v1_genomic.fna.gz --refList GCA_018820925.1_ASM1882092v1_genomic.fna/target_genomes.txt --output GCA_018820925.1_ASM1882092v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:29:24,688] [INFO] Task succeeded: fastANI
[2023-06-19 14:29:24,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62ef8dbb-32cd-4b30-bafa-0dc89ddcd603/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:29:24,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62ef8dbb-32cd-4b30-bafa-0dc89ddcd603/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:29:24,721] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:29:24,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:29:24,721] [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
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	79.9109	388	1122	95	below_threshold
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	77.903	238	1122	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.8135	197	1122	95	below_threshold
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	77.1197	174	1122	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.0362	148	1122	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.0296	151	1122	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.0227	163	1122	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	76.9556	158	1122	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	76.916	144	1122	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	76.8544	146	1122	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	76.851	158	1122	95	below_threshold
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	76.8402	141	1122	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	76.7186	124	1122	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.7184	144	1122	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.7143	132	1122	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.7132	129	1122	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	76.6868	117	1122	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	76.661	119	1122	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	76.6424	139	1122	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.6401	136	1122	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	76.506	146	1122	95	below_threshold
Burkholderia gladioli	strain=NBRC 13700	GCA_000739755.1	28095	28095	type	True	76.5047	151	1122	95	below_threshold
Burkholderia gladioli	strain=ATCC 10248	GCA_000959725.1	28095	28095	type	True	76.4789	154	1122	95	below_threshold
Paraburkholderia acidisoli	strain=DHF22	GCA_009789675.1	2571748	2571748	type	True	76.4204	112	1122	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	76.3578	109	1122	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	76.2818	79	1122	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	76.2724	78	1122	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	76.2643	90	1122	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:29:24,723] [INFO] DFAST Taxonomy check result was written to GCA_018820925.1_ASM1882092v1_genomic.fna/tc_result.tsv
[2023-06-19 14:29:24,724] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:29:24,724] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:29:24,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62ef8dbb-32cd-4b30-bafa-0dc89ddcd603/dqc_reference/checkm_data
[2023-06-19 14:29:24,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:29:24,763] [INFO] Task started: CheckM
[2023-06-19 14:29:24,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018820925.1_ASM1882092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018820925.1_ASM1882092v1_genomic.fna/checkm_input GCA_018820925.1_ASM1882092v1_genomic.fna/checkm_result
[2023-06-19 14:30:01,652] [INFO] Task succeeded: CheckM
[2023-06-19 14:30:01,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.65%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2023-06-19 14:30:01,687] [INFO] ===== Completeness check finished =====
[2023-06-19 14:30:01,688] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:30:01,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018820925.1_ASM1882092v1_genomic.fna/markers.fasta)
[2023-06-19 14:30:01,688] [INFO] Task started: Blastn
[2023-06-19 14:30:01,689] [INFO] Running command: blastn -query GCA_018820925.1_ASM1882092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62ef8dbb-32cd-4b30-bafa-0dc89ddcd603/dqc_reference/reference_markers_gtdb.fasta -out GCA_018820925.1_ASM1882092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:30:03,548] [INFO] Task succeeded: Blastn
[2023-06-19 14:30:03,554] [INFO] Selected 9 target genomes.
[2023-06-19 14:30:03,555] [INFO] Target genome list was writen to GCA_018820925.1_ASM1882092v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:30:03,590] [INFO] Task started: fastANI
[2023-06-19 14:30:03,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c9c1e7-4396-4675-89da-902e50632886/GCA_018820925.1_ASM1882092v1_genomic.fna.gz --refList GCA_018820925.1_ASM1882092v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018820925.1_ASM1882092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:30:09,780] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:09,794] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:30:09,794] [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
GCA_018820925.1	s__Sideroxydans sp018820925	100.0	1119	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.99	99.99	0.96	0.96	2	conclusive
GCA_016235045.1	s__Sideroxydans sp016235045	83.7594	709	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018813765.1	s__Sideroxydans sp018813765	82.8982	645	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.93	99.86	0.97	0.93	3	-
GCA_016208015.1	s__Sideroxydans sp016208015	82.7493	587	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214695.1	s__Sideroxydans sp016214695	82.5954	580	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445795.1	s__Sideroxydans sp003445795	82.5336	543	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025705.1	s__Sideroxydans lithotrophicus	81.9132	595	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791855.1	s__Sideroxydans sp013791855	80.0353	425	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.90	99.88	0.98	0.96	4	-
GCA_004297065.1	s__PALSA-1006 sp004297065	79.993	378	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__PALSA-1006	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 14:30:09,797] [INFO] GTDB search result was written to GCA_018820925.1_ASM1882092v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:30:09,797] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:30:09,804] [INFO] DFAST_QC result json was written to GCA_018820925.1_ASM1882092v1_genomic.fna/dqc_result.json
[2023-06-19 14:30:09,805] [INFO] DFAST_QC completed!
[2023-06-19 14:30:09,805] [INFO] Total running time: 0h1m18s