[2024-01-24 10:57:08,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:08,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:08,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ab8462c-28cc-4dc6-927e-d1d4dfe32052/dqc_reference
[2024-01-24 10:57:10,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:10,644] [INFO] Task started: Prodigal
[2024-01-24 10:57:10,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg43249917-0c38-44e5-97e5-a482d46a3ee8/GCF_018524365.1_ASM1852436v1_genomic.fna.gz | prodigal -d GCF_018524365.1_ASM1852436v1_genomic.fna/cds.fna -a GCF_018524365.1_ASM1852436v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:28,088] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:28,089] [INFO] Task started: HMMsearch
[2024-01-24 10:57:28,089] [INFO] Running command: hmmsearch --tblout GCF_018524365.1_ASM1852436v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ab8462c-28cc-4dc6-927e-d1d4dfe32052/dqc_reference/reference_markers.hmm GCF_018524365.1_ASM1852436v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:28,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:28,427] [INFO] Found 6/6 markers.
[2024-01-24 10:57:28,475] [INFO] Query marker FASTA was written to GCF_018524365.1_ASM1852436v1_genomic.fna/markers.fasta
[2024-01-24 10:57:28,475] [INFO] Task started: Blastn
[2024-01-24 10:57:28,475] [INFO] Running command: blastn -query GCF_018524365.1_ASM1852436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab8462c-28cc-4dc6-927e-d1d4dfe32052/dqc_reference/reference_markers.fasta -out GCF_018524365.1_ASM1852436v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:29,532] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:29,535] [INFO] Selected 20 target genomes.
[2024-01-24 10:57:29,535] [INFO] Target genome list was writen to GCF_018524365.1_ASM1852436v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:29,582] [INFO] Task started: fastANI
[2024-01-24 10:57:29,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg43249917-0c38-44e5-97e5-a482d46a3ee8/GCF_018524365.1_ASM1852436v1_genomic.fna.gz --refList GCF_018524365.1_ASM1852436v1_genomic.fna/target_genomes.txt --output GCF_018524365.1_ASM1852436v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:48,964] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:48,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ab8462c-28cc-4dc6-927e-d1d4dfe32052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:48,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ab8462c-28cc-4dc6-927e-d1d4dfe32052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:48,982] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:48,982] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:48,982] [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
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	81.7155	833	1659	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	80.4729	553	1659	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	80.0406	639	1659	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.934	581	1659	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	79.8796	661	1659	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	79.8137	567	1659	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	79.7938	649	1659	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	79.762	535	1659	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	79.7536	552	1659	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	79.7085	535	1659	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	79.6913	537	1659	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	79.6866	559	1659	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	79.5739	614	1659	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.4836	594	1659	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	79.4525	608	1659	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	79.2803	602	1659	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	79.1685	632	1659	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	79.0859	642	1659	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.8548	475	1659	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.7154	454	1659	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:48,984] [INFO] DFAST Taxonomy check result was written to GCF_018524365.1_ASM1852436v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:48,984] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:48,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:48,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ab8462c-28cc-4dc6-927e-d1d4dfe32052/dqc_reference/checkm_data
[2024-01-24 10:57:48,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:49,036] [INFO] Task started: CheckM
[2024-01-24 10:57:49,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018524365.1_ASM1852436v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018524365.1_ASM1852436v1_genomic.fna/checkm_input GCF_018524365.1_ASM1852436v1_genomic.fna/checkm_result
[2024-01-24 10:58:51,957] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:51,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:51,976] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:51,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:51,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018524365.1_ASM1852436v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:51,977] [INFO] Task started: Blastn
[2024-01-24 10:58:51,978] [INFO] Running command: blastn -query GCF_018524365.1_ASM1852436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab8462c-28cc-4dc6-927e-d1d4dfe32052/dqc_reference/reference_markers_gtdb.fasta -out GCF_018524365.1_ASM1852436v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:54,123] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:54,127] [INFO] Selected 10 target genomes.
[2024-01-24 10:58:54,127] [INFO] Target genome list was writen to GCF_018524365.1_ASM1852436v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:54,148] [INFO] Task started: fastANI
[2024-01-24 10:58:54,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg43249917-0c38-44e5-97e5-a482d46a3ee8/GCF_018524365.1_ASM1852436v1_genomic.fna.gz --refList GCF_018524365.1_ASM1852436v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018524365.1_ASM1852436v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:04,699] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:04,722] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:04,723] [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_018524365.1	s__Denitromonas sp018524365	100.0	1657	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008501585.1	s__Denitromonas sp008501585	87.2276	1122	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007625205.1	s__Denitromonas halophilus	85.1702	1059	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	98.77	98.30	0.95	0.94	5	-
GCF_007625155.1	s__Denitromonas halophilus_A	85.0548	1054	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010983895.1	s__Denitromonas sp010983895	81.7239	831	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489115.1	s__Thauera_A sp014489115	80.7141	699	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018240785.1	s__Thauera sp018240785	79.767	573	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469605.1	s__Zoogloea sp009469605	79.4224	583	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911025.1	s__Azoarcus sp012911025	79.1202	588	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821865.1	s__PNJM01 sp013821865	78.2893	274	1659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__PNJM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:04,725] [INFO] GTDB search result was written to GCF_018524365.1_ASM1852436v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:04,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:04,730] [INFO] DFAST_QC result json was written to GCF_018524365.1_ASM1852436v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:04,730] [INFO] DFAST_QC completed!
[2024-01-24 10:59:04,730] [INFO] Total running time: 0h1m57s