[2024-01-24 13:01:39,625] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg6aa7beb1-a217-40bc-a61b-80524d759490/dqc_reference
[2024-01-24 13:01:41,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,310] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg05efd06a-72c9-4342-aa2a-a44faf049437/GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/cds.fna -a GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:00,265] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:00,265] [INFO] Task started: HMMsearch
[2024-01-24 13:02:00,265] [INFO] Running command: hmmsearch --tblout GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6aa7beb1-a217-40bc-a61b-80524d759490/dqc_reference/reference_markers.hmm GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:00,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:00,666] [INFO] Found 6/6 markers.
[2024-01-24 13:02:00,733] [INFO] Query marker FASTA was written to GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:02:00,734] [INFO] Task started: Blastn
[2024-01-24 13:02:00,734] [INFO] Running command: blastn -query GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6aa7beb1-a217-40bc-a61b-80524d759490/dqc_reference/reference_markers.fasta -out GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:01,858] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:01,862] [INFO] Selected 27 target genomes.
[2024-01-24 13:02:01,862] [INFO] Target genome list was writen to GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:02:01,872] [INFO] Task started: fastANI
[2024-01-24 13:02:01,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg05efd06a-72c9-4342-aa2a-a44faf049437/GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna.gz --refList GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:40,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:40,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6aa7beb1-a217-40bc-a61b-80524d759490/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:40,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6aa7beb1-a217-40bc-a61b-80524d759490/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:40,391] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:40,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:40,392] [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
Pseudomonas graminis	strain=DSM 11363	GCA_900111735.1	158627	158627	suspected-type	True	100.0	1893	1899	95	conclusive
Pseudomonas abietaniphila	strain=ATCC 700689	GCA_900100795.1	89065	89065	type	True	83.772	1304	1899	95	below_threshold
Pseudomonas bohemica	strain=IA19	GCA_002934685.1	2044872	2044872	type	True	83.5336	1265	1899	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=CCUG 712	GCA_008801625.1	587851	587753	type	True	81.3598	958	1899	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	81.3395	954	1899	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	81.3233	971	1899	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	81.27	967	1899	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	81.2661	929	1899	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP8903	GCA_001400595.1	251701	251701	pathovar	True	81.2177	941	1899	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.2009	962	1899	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=CFBP 1702	GCA_000935765.1	251701	251701	pathovar	True	81.1819	955	1899	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	81.1548	982	1899	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4303	GCA_001401395.1	251701	251701	pathovar	True	81.1344	937	1899	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4116	GCA_001401405.1	251701	251701	pathovar	True	81.1229	945	1899	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	80.9591	866	1899	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	80.9472	913	1899	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	80.8506	925	1899	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	80.829	925	1899	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	80.7262	849	1899	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	80.6947	855	1899	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	80.6768	860	1899	95	below_threshold
Pseudomonas synxantha	strain=LMG 2190	GCA_900105675.1	47883	47883	type	True	80.5149	881	1899	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	80.3386	771	1899	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	78.9595	493	1899	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.904	461	1899	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	78.8438	512	1899	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	78.8241	679	1899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,394] [INFO] DFAST Taxonomy check result was written to GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:02:40,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:40,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:40,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6aa7beb1-a217-40bc-a61b-80524d759490/dqc_reference/checkm_data
[2024-01-24 13:02:40,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:40,456] [INFO] Task started: CheckM
[2024-01-24 13:02:40,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/checkm_input GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:03:34,428] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:34,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:34,454] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:34,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:34,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:03:34,456] [INFO] Task started: Blastn
[2024-01-24 13:03:34,456] [INFO] Running command: blastn -query GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6aa7beb1-a217-40bc-a61b-80524d759490/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:35,876] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:35,881] [INFO] Selected 9 target genomes.
[2024-01-24 13:03:35,882] [INFO] Target genome list was writen to GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:35,888] [INFO] Task started: fastANI
[2024-01-24 13:03:35,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg05efd06a-72c9-4342-aa2a-a44faf049437/GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna.gz --refList GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:51,789] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:51,797] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:51,797] [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_900111735.1	s__Pseudomonas_E graminis	100.0	1893	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.28	98.01	0.93	0.92	4	conclusive
GCF_001705435.1	s__Pseudomonas_E graminis_B	92.7544	1628	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.17	98.17	0.90	0.90	2	-
GCF_004364335.1	s__Pseudomonas_E graminis_D	92.471	1685	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842265.1	s__Pseudomonas_E sp014842265	92.0731	1665	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013201545.1	s__Pseudomonas_E sp900585815	91.6591	1617	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.31	96.17	0.93	0.92	5	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	78.953	453	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	78.9414	495	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	78.8076	670	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_002286785.1	s__Pseudomonas_M sp002286785	78.7914	590	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:51,799] [INFO] GTDB search result was written to GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:51,799] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:51,807] [INFO] DFAST_QC result json was written to GCF_900111735.1_IMG-taxon_2671180035_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:03:51,807] [INFO] DFAST_QC completed!
[2024-01-24 13:03:51,807] [INFO] Total running time: 0h2m12s