[2024-01-24 15:10:20,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,118] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5293f10-783d-49ce-b5c3-d156484af973/dqc_reference
[2024-01-24 15:10:22,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,722] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg429c3f97-3b9d-477d-80a7-859a8fde9519/GCF_003568845.1_ASM356884v1_genomic.fna.gz | prodigal -d GCF_003568845.1_ASM356884v1_genomic.fna/cds.fna -a GCF_003568845.1_ASM356884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:39,866] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:39,866] [INFO] Task started: HMMsearch
[2024-01-24 15:10:39,866] [INFO] Running command: hmmsearch --tblout GCF_003568845.1_ASM356884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5293f10-783d-49ce-b5c3-d156484af973/dqc_reference/reference_markers.hmm GCF_003568845.1_ASM356884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:40,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:40,159] [INFO] Found 6/6 markers.
[2024-01-24 15:10:40,205] [INFO] Query marker FASTA was written to GCF_003568845.1_ASM356884v1_genomic.fna/markers.fasta
[2024-01-24 15:10:40,205] [INFO] Task started: Blastn
[2024-01-24 15:10:40,205] [INFO] Running command: blastn -query GCF_003568845.1_ASM356884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5293f10-783d-49ce-b5c3-d156484af973/dqc_reference/reference_markers.fasta -out GCF_003568845.1_ASM356884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:41,117] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:41,122] [INFO] Selected 25 target genomes.
[2024-01-24 15:10:41,122] [INFO] Target genome list was writen to GCF_003568845.1_ASM356884v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:41,138] [INFO] Task started: fastANI
[2024-01-24 15:10:41,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg429c3f97-3b9d-477d-80a7-859a8fde9519/GCF_003568845.1_ASM356884v1_genomic.fna.gz --refList GCF_003568845.1_ASM356884v1_genomic.fna/target_genomes.txt --output GCF_003568845.1_ASM356884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:07,009] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:07,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5293f10-783d-49ce-b5c3-d156484af973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:07,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5293f10-783d-49ce-b5c3-d156484af973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:07,029] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:11:07,029] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:11:07,029] [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
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	78.7938	522	1789	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	78.6827	525	1789	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	78.551	516	1789	95	below_threshold
Niveispirillum cyanobacteriorum	strain=TH16	GCA_002868735.1	1612173	1612173	type	True	78.5084	505	1789	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	78.4691	527	1789	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	78.4339	488	1789	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	78.4109	494	1789	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	78.3906	553	1789	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	78.2851	492	1789	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	78.2838	481	1789	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	78.2828	502	1789	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	78.1632	531	1789	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	78.1106	530	1789	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	78.0901	497	1789	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	78.0846	522	1789	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	78.0045	523	1789	95	below_threshold
Niveispirillum lacus	strain=1-14	GCA_002251795.1	1981099	1981099	type	True	77.8979	373	1789	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	77.7534	426	1789	95	below_threshold
Paracoccus suum	strain=SC2-6	GCA_003324675.1	2259340	2259340	type	True	76.7716	119	1789	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.6745	144	1789	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.6164	233	1789	95	below_threshold
Caulobacter henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	76.6126	154	1789	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	76.607	205	1789	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.4334	136	1789	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	76.3837	347	1789	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:07,031] [INFO] DFAST Taxonomy check result was written to GCF_003568845.1_ASM356884v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:07,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:07,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:07,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5293f10-783d-49ce-b5c3-d156484af973/dqc_reference/checkm_data
[2024-01-24 15:11:07,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:07,092] [INFO] Task started: CheckM
[2024-01-24 15:11:07,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003568845.1_ASM356884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003568845.1_ASM356884v1_genomic.fna/checkm_input GCF_003568845.1_ASM356884v1_genomic.fna/checkm_result
[2024-01-24 15:12:01,068] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:01,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:01,090] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:01,090] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:01,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003568845.1_ASM356884v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:01,091] [INFO] Task started: Blastn
[2024-01-24 15:12:01,091] [INFO] Running command: blastn -query GCF_003568845.1_ASM356884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5293f10-783d-49ce-b5c3-d156484af973/dqc_reference/reference_markers_gtdb.fasta -out GCF_003568845.1_ASM356884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:02,811] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:02,814] [INFO] Selected 17 target genomes.
[2024-01-24 15:12:02,814] [INFO] Target genome list was writen to GCF_003568845.1_ASM356884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:02,864] [INFO] Task started: fastANI
[2024-01-24 15:12:02,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg429c3f97-3b9d-477d-80a7-859a8fde9519/GCF_003568845.1_ASM356884v1_genomic.fna.gz --refList GCF_003568845.1_ASM356884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003568845.1_ASM356884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:22,190] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:22,209] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:22,209] [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_003568845.1	s__Indioceanicola profundi	100.0	1787	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Indioceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001939945.1	s__Aerophototrophica crusticola	80.4846	803	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Aerophototrophica	95.0	99.94	99.94	0.97	0.97	2	-
GCF_014197805.1	s__Rhodospirillum_A centenum	80.3257	704	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003336875.1	s__Oleisolibacter albus	80.3217	701	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730165.1	s__Nitrospirillum amazonense	78.9298	521	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
GCF_007828035.1	s__Nitrospirillum amazonense_A	78.7782	505	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	78.7056	524	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828045.1	s__Nitrospirillum amazonense_C	78.676	537	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017996735.1	s__Niveispirillum sp017996735	78.5534	523	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868735.1	s__Niveispirillum cyanobacteriorum	78.5447	506	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188385.1	s__Niveispirillum sp900188385	78.5187	504	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009495745.1	s__Niveispirillum sp009495745	78.4414	494	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876155.1	s__Azospirillum rugosum	78.4397	528	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429645.1	s__Niveispirillum irakense	78.4095	494	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	78.332	502	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_017876165.1	s__Azospirillum soli	78.2826	492	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691025.1	s__SHWB01 sp009691025	76.3992	113	1789	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__SHWB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:22,211] [INFO] GTDB search result was written to GCF_003568845.1_ASM356884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:22,212] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:22,217] [INFO] DFAST_QC result json was written to GCF_003568845.1_ASM356884v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:22,217] [INFO] DFAST_QC completed!
[2024-01-24 15:12:22,217] [INFO] Total running time: 0h2m2s