[2023-06-28 18:56:33,274] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:56:33,276] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:56:33,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg9921b2ca-da0a-4361-9c7e-868feefc2b2a/dqc_reference
[2023-06-28 18:56:34,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:56:34,470] [INFO] Task started: Prodigal
[2023-06-28 18:56:34,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg133d0132-be29-4929-b585-d2e0fa4caf53/GCA_020445895.1_ASM2044589v1_genomic.fna.gz | prodigal -d GCA_020445895.1_ASM2044589v1_genomic.fna/cds.fna -a GCA_020445895.1_ASM2044589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:56:44,857] [INFO] Task succeeded: Prodigal
[2023-06-28 18:56:44,857] [INFO] Task started: HMMsearch
[2023-06-28 18:56:44,857] [INFO] Running command: hmmsearch --tblout GCA_020445895.1_ASM2044589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9921b2ca-da0a-4361-9c7e-868feefc2b2a/dqc_reference/reference_markers.hmm GCA_020445895.1_ASM2044589v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:56:45,122] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:56:45,123] [INFO] Found 6/6 markers.
[2023-06-28 18:56:45,159] [INFO] Query marker FASTA was written to GCA_020445895.1_ASM2044589v1_genomic.fna/markers.fasta
[2023-06-28 18:56:45,160] [INFO] Task started: Blastn
[2023-06-28 18:56:45,160] [INFO] Running command: blastn -query GCA_020445895.1_ASM2044589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9921b2ca-da0a-4361-9c7e-868feefc2b2a/dqc_reference/reference_markers.fasta -out GCA_020445895.1_ASM2044589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:56:46,145] [INFO] Task succeeded: Blastn
[2023-06-28 18:56:46,149] [INFO] Selected 23 target genomes.
[2023-06-28 18:56:46,149] [INFO] Target genome list was writen to GCA_020445895.1_ASM2044589v1_genomic.fna/target_genomes.txt
[2023-06-28 18:56:46,150] [INFO] Task started: fastANI
[2023-06-28 18:56:46,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg133d0132-be29-4929-b585-d2e0fa4caf53/GCA_020445895.1_ASM2044589v1_genomic.fna.gz --refList GCA_020445895.1_ASM2044589v1_genomic.fna/target_genomes.txt --output GCA_020445895.1_ASM2044589v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:57:03,424] [INFO] Task succeeded: fastANI
[2023-06-28 18:57:03,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9921b2ca-da0a-4361-9c7e-868feefc2b2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:57:03,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9921b2ca-da0a-4361-9c7e-868feefc2b2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:57:03,443] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:57:03,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:57:03,444] [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	79.7544	530	1017	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.9562	392	1017	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.7301	350	1017	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.6222	332	1017	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.5463	299	1017	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.5241	305	1017	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	78.3943	304	1017	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.3857	302	1017	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	78.3729	307	1017	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	78.3622	304	1017	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	78.3522	315	1017	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	78.142	298	1017	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	78.1201	305	1017	95	below_threshold
Thauera terpenica	strain=58Eu	GCA_000443165.1	76113	76113	type	True	78.0189	261	1017	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	77.9284	270	1017	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	77.7931	256	1017	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	77.7586	257	1017	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.701	247	1017	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	77.6651	239	1017	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	77.6068	266	1017	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.1846	196	1017	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	77.1564	195	1017	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	74.9495	50	1017	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:57:03,446] [INFO] DFAST Taxonomy check result was written to GCA_020445895.1_ASM2044589v1_genomic.fna/tc_result.tsv
[2023-06-28 18:57:03,446] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:57:03,447] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:57:03,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9921b2ca-da0a-4361-9c7e-868feefc2b2a/dqc_reference/checkm_data
[2023-06-28 18:57:03,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:57:03,493] [INFO] Task started: CheckM
[2023-06-28 18:57:03,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020445895.1_ASM2044589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020445895.1_ASM2044589v1_genomic.fna/checkm_input GCA_020445895.1_ASM2044589v1_genomic.fna/checkm_result
[2023-06-28 18:57:41,355] [INFO] Task succeeded: CheckM
[2023-06-28 18:57:41,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.14%
Contamintation: 9.26%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:57:41,378] [INFO] ===== Completeness check finished =====
[2023-06-28 18:57:41,379] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:57:41,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020445895.1_ASM2044589v1_genomic.fna/markers.fasta)
[2023-06-28 18:57:41,380] [INFO] Task started: Blastn
[2023-06-28 18:57:41,380] [INFO] Running command: blastn -query GCA_020445895.1_ASM2044589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9921b2ca-da0a-4361-9c7e-868feefc2b2a/dqc_reference/reference_markers_gtdb.fasta -out GCA_020445895.1_ASM2044589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:57:43,245] [INFO] Task succeeded: Blastn
[2023-06-28 18:57:43,250] [INFO] Selected 11 target genomes.
[2023-06-28 18:57:43,250] [INFO] Target genome list was writen to GCA_020445895.1_ASM2044589v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:57:43,260] [INFO] Task started: fastANI
[2023-06-28 18:57:43,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg133d0132-be29-4929-b585-d2e0fa4caf53/GCA_020445895.1_ASM2044589v1_genomic.fna.gz --refList GCA_020445895.1_ASM2044589v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020445895.1_ASM2044589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:57:52,582] [INFO] Task succeeded: fastANI
[2023-06-28 18:57:52,598] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:57:52,598] [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_007625205.1	s__Denitromonas halophilus	88.8977	895	1017	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	88.6546	896	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501585.1	s__Denitromonas sp008501585	84.9126	841	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018524365.1	s__Denitromonas sp018524365	84.2675	808	1017	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	79.7892	526	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309585.1	s__Denitromonas sp017309585	78.9565	392	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	98.28	98.28	0.96	0.96	2	-
GCF_012910905.1	s__Aromatoleum toluvorans	78.3602	308	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911005.1	s__Aromatoleum toluolicum	78.3428	306	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000443165.1	s__Thauera terpenica	78.023	260	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910705.1	s__Aromatoleum anaerobium	77.8763	268	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197755.1	s__Rhodocyclus tenuis	77.1564	195	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.79	97.58	0.96	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-28 18:57:52,600] [INFO] GTDB search result was written to GCA_020445895.1_ASM2044589v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:57:52,600] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:57:52,604] [INFO] DFAST_QC result json was written to GCA_020445895.1_ASM2044589v1_genomic.fna/dqc_result.json
[2023-06-28 18:57:52,605] [INFO] DFAST_QC completed!
[2023-06-28 18:57:52,605] [INFO] Total running time: 0h1m19s