[2024-01-24 14:23:05,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:05,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:05,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg82e15d15-4651-474c-bf7b-4f882b4f9338/dqc_reference
[2024-01-24 14:23:06,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,365] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,365] [INFO] Running command: gunzip -c /var/lib/cwl/stge1469d3b-01bf-4772-8cb1-1aaaad95f93a/GCF_025961205.1_ASM2596120v1_genomic.fna.gz | prodigal -d GCF_025961205.1_ASM2596120v1_genomic.fna/cds.fna -a GCF_025961205.1_ASM2596120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:27,552] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:27,552] [INFO] Task started: HMMsearch
[2024-01-24 14:23:27,552] [INFO] Running command: hmmsearch --tblout GCF_025961205.1_ASM2596120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82e15d15-4651-474c-bf7b-4f882b4f9338/dqc_reference/reference_markers.hmm GCF_025961205.1_ASM2596120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:27,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:27,960] [INFO] Found 6/6 markers.
[2024-01-24 14:23:28,010] [INFO] Query marker FASTA was written to GCF_025961205.1_ASM2596120v1_genomic.fna/markers.fasta
[2024-01-24 14:23:28,010] [INFO] Task started: Blastn
[2024-01-24 14:23:28,011] [INFO] Running command: blastn -query GCF_025961205.1_ASM2596120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82e15d15-4651-474c-bf7b-4f882b4f9338/dqc_reference/reference_markers.fasta -out GCF_025961205.1_ASM2596120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:29,053] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:29,057] [INFO] Selected 20 target genomes.
[2024-01-24 14:23:29,057] [INFO] Target genome list was writen to GCF_025961205.1_ASM2596120v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:29,077] [INFO] Task started: fastANI
[2024-01-24 14:23:29,077] [INFO] Running command: fastANI --query /var/lib/cwl/stge1469d3b-01bf-4772-8cb1-1aaaad95f93a/GCF_025961205.1_ASM2596120v1_genomic.fna.gz --refList GCF_025961205.1_ASM2596120v1_genomic.fna/target_genomes.txt --output GCF_025961205.1_ASM2596120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:59,844] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:59,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82e15d15-4651-474c-bf7b-4f882b4f9338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:59,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82e15d15-4651-474c-bf7b-4f882b4f9338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:59,866] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:59,867] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:59,867] [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
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	80.7283	970	1961	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	80.6978	968	1961	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	80.5709	1000	1961	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	80.5652	949	1961	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	80.544	825	1961	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	80.4792	886	1961	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	80.3853	905	1961	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	80.3468	1023	1961	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	80.3464	912	1961	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	80.2518	930	1961	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	80.2455	902	1961	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	80.2015	924	1961	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	80.1619	912	1961	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	80.106	882	1961	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	80.0455	926	1961	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	79.9426	912	1961	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	79.806	836	1961	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	79.7995	853	1961	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	77.5538	453	1961	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3434	424	1961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:59,869] [INFO] DFAST Taxonomy check result was written to GCF_025961205.1_ASM2596120v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:59,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:59,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:59,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82e15d15-4651-474c-bf7b-4f882b4f9338/dqc_reference/checkm_data
[2024-01-24 14:23:59,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:59,932] [INFO] Task started: CheckM
[2024-01-24 14:23:59,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025961205.1_ASM2596120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025961205.1_ASM2596120v1_genomic.fna/checkm_input GCF_025961205.1_ASM2596120v1_genomic.fna/checkm_result
[2024-01-24 14:25:26,949] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:26,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:26,978] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:26,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:26,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025961205.1_ASM2596120v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:26,979] [INFO] Task started: Blastn
[2024-01-24 14:25:26,979] [INFO] Running command: blastn -query GCF_025961205.1_ASM2596120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82e15d15-4651-474c-bf7b-4f882b4f9338/dqc_reference/reference_markers_gtdb.fasta -out GCF_025961205.1_ASM2596120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:28,860] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:28,865] [INFO] Selected 17 target genomes.
[2024-01-24 14:25:28,865] [INFO] Target genome list was writen to GCF_025961205.1_ASM2596120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:28,953] [INFO] Task started: fastANI
[2024-01-24 14:25:28,953] [INFO] Running command: fastANI --query /var/lib/cwl/stge1469d3b-01bf-4772-8cb1-1aaaad95f93a/GCF_025961205.1_ASM2596120v1_genomic.fna.gz --refList GCF_025961205.1_ASM2596120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025961205.1_ASM2596120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:56,863] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:56,889] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:25:56,890] [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_008365375.1	s__Azospirillum sp008365375	80.6557	914	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876155.1	s__Azospirillum rugosum	80.5423	956	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	80.5037	943	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_000283655.1	s__Azospirillum lipoferum_C	80.4817	919	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116095.1	s__Azospirillum sp003116095	80.476	977	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233655.1	s__Azospirillum ramasamyi	80.4292	892	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	80.3596	1022	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_900177515.1	s__Azospirillum oryzae_A	80.3375	928	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	80.2732	944	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429625.1	s__Azospirillum halopraeferens	80.2202	934	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639105.2	s__Azospirillum humicireducens	80.2099	909	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989665.1	s__Azospirillum doebereinerae	80.1451	913	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364795.1	s__Azospirillum oryzae	80.0607	889	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_000010725.1	s__Azospirillum lipoferum_B	80.0441	967	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	79.9901	916	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364955.1	s__Azospirillum lipoferum	79.9008	920	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	79.8287	850	1961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:56,892] [INFO] GTDB search result was written to GCF_025961205.1_ASM2596120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:56,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:56,897] [INFO] DFAST_QC result json was written to GCF_025961205.1_ASM2596120v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:56,897] [INFO] DFAST_QC completed!
[2024-01-24 14:25:56,897] [INFO] Total running time: 0h2m52s