[2024-01-24 11:59:51,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a300807-5a72-4b51-ac51-0ffe0f95ad02/dqc_reference
[2024-01-24 11:59:55,389] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,390] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,390] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f8022b5-631c-4561-bd61-a92609598615/GCF_018324385.1_ASM1832438v1_genomic.fna.gz | prodigal -d GCF_018324385.1_ASM1832438v1_genomic.fna/cds.fna -a GCF_018324385.1_ASM1832438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:04,416] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:04,416] [INFO] Task started: HMMsearch
[2024-01-24 12:00:04,417] [INFO] Running command: hmmsearch --tblout GCF_018324385.1_ASM1832438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a300807-5a72-4b51-ac51-0ffe0f95ad02/dqc_reference/reference_markers.hmm GCF_018324385.1_ASM1832438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:04,667] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:04,668] [INFO] Found 6/6 markers.
[2024-01-24 12:00:04,695] [INFO] Query marker FASTA was written to GCF_018324385.1_ASM1832438v1_genomic.fna/markers.fasta
[2024-01-24 12:00:04,696] [INFO] Task started: Blastn
[2024-01-24 12:00:04,696] [INFO] Running command: blastn -query GCF_018324385.1_ASM1832438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a300807-5a72-4b51-ac51-0ffe0f95ad02/dqc_reference/reference_markers.fasta -out GCF_018324385.1_ASM1832438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:05,685] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:05,694] [INFO] Selected 26 target genomes.
[2024-01-24 12:00:05,695] [INFO] Target genome list was writen to GCF_018324385.1_ASM1832438v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:05,731] [INFO] Task started: fastANI
[2024-01-24 12:00:05,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8022b5-631c-4561-bd61-a92609598615/GCF_018324385.1_ASM1832438v1_genomic.fna.gz --refList GCF_018324385.1_ASM1832438v1_genomic.fna/target_genomes.txt --output GCF_018324385.1_ASM1832438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:22,406] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:22,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a300807-5a72-4b51-ac51-0ffe0f95ad02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:22,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a300807-5a72-4b51-ac51-0ffe0f95ad02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:22,427] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:22,427] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:22,427] [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	100.0	856	857	95	conclusive
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	78.8603	263	857	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.9641	243	857	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	77.9154	194	857	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	77.8911	203	857	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.7714	236	857	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	77.6611	179	857	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.6382	204	857	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.6318	195	857	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.5918	183	857	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	77.5135	164	857	95	below_threshold
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	77.4788	182	857	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	77.4116	199	857	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	77.3702	191	857	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	77.3319	195	857	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	77.2911	192	857	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	77.2622	189	857	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.2315	195	857	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	77.214	209	857	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	77.1844	189	857	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	77.1778	120	857	95	below_threshold
Paludibacterium paludis	strain=BCRC 80514	GCA_018802605.1	1225769	1225769	type	True	77.1658	115	857	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	77.1296	152	857	95	below_threshold
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	76.8802	77	857	95	below_threshold
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	76.6764	117	857	95	below_threshold
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	76.636	97	857	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:22,430] [INFO] DFAST Taxonomy check result was written to GCF_018324385.1_ASM1832438v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:22,430] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:22,431] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:22,431] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a300807-5a72-4b51-ac51-0ffe0f95ad02/dqc_reference/checkm_data
[2024-01-24 12:00:22,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:22,461] [INFO] Task started: CheckM
[2024-01-24 12:00:22,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018324385.1_ASM1832438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018324385.1_ASM1832438v1_genomic.fna/checkm_input GCF_018324385.1_ASM1832438v1_genomic.fna/checkm_result
[2024-01-24 12:00:53,026] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:53,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:53,051] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:53,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:53,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018324385.1_ASM1832438v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:53,052] [INFO] Task started: Blastn
[2024-01-24 12:00:53,053] [INFO] Running command: blastn -query GCF_018324385.1_ASM1832438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a300807-5a72-4b51-ac51-0ffe0f95ad02/dqc_reference/reference_markers_gtdb.fasta -out GCF_018324385.1_ASM1832438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:54,934] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:54,938] [INFO] Selected 19 target genomes.
[2024-01-24 12:00:54,938] [INFO] Target genome list was writen to GCF_018324385.1_ASM1832438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:54,968] [INFO] Task started: fastANI
[2024-01-24 12:00:54,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8022b5-631c-4561-bd61-a92609598615/GCF_018324385.1_ASM1832438v1_genomic.fna.gz --refList GCF_018324385.1_ASM1832438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018324385.1_ASM1832438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:04,232] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:04,259] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:04,260] [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_018324385.1	s__Gallionella kumadai	100.0	855	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001801085.1	s__Gallionella sp001801085	82.8416	439	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.85	99.85	0.92	0.92	2	-
GCA_001801105.1	s__Gallionella sp001801105	82.6987	394	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716325.1	s__Gallionella sp016716325	81.7471	430	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183575.1	s__Gallionella sp016183575	81.6036	289	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177795.1	s__Gallionella sp016177795	81.0549	302	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218415.1	s__Gallionella sp016218415	81.0128	395	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801215.1	s__Gallionella sp001801215	80.9487	432	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.86	99.86	0.90	0.90	2	-
GCA_016208015.1	s__Sideroxydans sp016208015	80.8839	432	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197305.1	s__Gallionella sp016197305	80.8301	338	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235045.1	s__Sideroxydans sp016235045	80.5583	424	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801175.1	s__Gallionella sp001801175	80.2906	351	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620315.1	s__Sideroxydans sp011620315	80.1933	361	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801055.1	s__Gallionella sp001801055	79.8692	257	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819205.1	s__Sideroxydans sp018819205	79.6145	291	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.83	99.83	0.84	0.84	2	-
GCA_016195965.1	s__Gallionella sp016195965	79.3938	329	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858965.1	s__Gallionella sp903858965	79.3219	285	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.89	99.89	0.95	0.95	2	-
GCA_016234685.1	s__Ferriphaselus sp016234685	79.2935	330	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Ferriphaselus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002787455.1	s__Sideroxydans sp002787455	79.2372	174	857	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.23	98.87	0.83	0.78	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:04,262] [INFO] GTDB search result was written to GCF_018324385.1_ASM1832438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:04,263] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:04,267] [INFO] DFAST_QC result json was written to GCF_018324385.1_ASM1832438v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:04,267] [INFO] DFAST_QC completed!
[2024-01-24 12:01:04,268] [INFO] Total running time: 0h1m12s