[2024-01-25 17:34:07,126] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,129] [INFO] DQC Reference Directory: /var/lib/cwl/stge5ba1a1c-7f32-4ee7-95b6-0271348cde63/dqc_reference
[2024-01-25 17:34:08,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,950] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg282f04cd-98be-410b-886d-8be792e79fc5/GCF_014357575.1_ASM1435757v1_genomic.fna.gz | prodigal -d GCF_014357575.1_ASM1435757v1_genomic.fna/cds.fna -a GCF_014357575.1_ASM1435757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:24,627] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:24,628] [INFO] Task started: HMMsearch
[2024-01-25 17:34:24,628] [INFO] Running command: hmmsearch --tblout GCF_014357575.1_ASM1435757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5ba1a1c-7f32-4ee7-95b6-0271348cde63/dqc_reference/reference_markers.hmm GCF_014357575.1_ASM1435757v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:24,937] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:24,938] [INFO] Found 6/6 markers.
[2024-01-25 17:34:24,983] [INFO] Query marker FASTA was written to GCF_014357575.1_ASM1435757v1_genomic.fna/markers.fasta
[2024-01-25 17:34:24,983] [INFO] Task started: Blastn
[2024-01-25 17:34:24,983] [INFO] Running command: blastn -query GCF_014357575.1_ASM1435757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5ba1a1c-7f32-4ee7-95b6-0271348cde63/dqc_reference/reference_markers.fasta -out GCF_014357575.1_ASM1435757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:25,812] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:25,815] [INFO] Selected 31 target genomes.
[2024-01-25 17:34:25,815] [INFO] Target genome list was writen to GCF_014357575.1_ASM1435757v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:25,839] [INFO] Task started: fastANI
[2024-01-25 17:34:25,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg282f04cd-98be-410b-886d-8be792e79fc5/GCF_014357575.1_ASM1435757v1_genomic.fna.gz --refList GCF_014357575.1_ASM1435757v1_genomic.fna/target_genomes.txt --output GCF_014357575.1_ASM1435757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:59,501] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:59,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5ba1a1c-7f32-4ee7-95b6-0271348cde63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:59,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5ba1a1c-7f32-4ee7-95b6-0271348cde63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:59,519] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:34:59,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:34:59,520] [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 cichorii	strain=DSM 50259	GCA_018343775.1	36746	36746	suspected-type	True	81.5934	984	1842	95	below_threshold
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	81.5882	973	1842	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	81.5267	982	1842	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	81.5192	943	1842	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	81.5119	929	1842	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	81.4871	906	1842	95	below_threshold
Pseudomonas viridiflava	strain=ICMP2848	GCA_001401215.1	33069	33069	type	True	81.4683	934	1842	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP2814	GCA_001401385.1	251701	251701	pathovar	True	81.4138	909	1842	95	below_threshold
Pseudomonas avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	81.4086	899	1842	95	below_threshold
Pseudomonas syringae pv. coryli	strain=NCPPB 4273	GCA_000972175.1	317659	317659	pathovar	True	81.4041	934	1842	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	81.3981	751	1842	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000444135.1	46257	46257	type	True	81.3847	879	1842	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4116	GCA_001401405.1	251701	251701	pathovar	True	81.3841	925	1842	95	below_threshold
Pseudomonas viridiflava	strain=ICMP 2848	GCA_001642795.1	33069	33069	type	True	81.3784	987	1842	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	81.3666	948	1842	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP8903	GCA_001400595.1	251701	251701	pathovar	True	81.3551	922	1842	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	81.3505	963	1842	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP529	GCA_001400335.1	251701	251701	pathovar	True	81.3459	906	1842	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	81.3383	955	1842	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	80.7988	720	1842	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	80.7986	836	1842	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	80.7946	765	1842	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	80.7104	813	1842	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	80.673	776	1842	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	80.5996	809	1842	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	80.5829	733	1842	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	80.5626	814	1842	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	80.5444	725	1842	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	80.5417	741	1842	95	below_threshold
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	80.5397	737	1842	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	80.056	591	1842	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:59,522] [INFO] DFAST Taxonomy check result was written to GCF_014357575.1_ASM1435757v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:59,523] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:59,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:59,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5ba1a1c-7f32-4ee7-95b6-0271348cde63/dqc_reference/checkm_data
[2024-01-25 17:34:59,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:59,582] [INFO] Task started: CheckM
[2024-01-25 17:34:59,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014357575.1_ASM1435757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014357575.1_ASM1435757v1_genomic.fna/checkm_input GCF_014357575.1_ASM1435757v1_genomic.fna/checkm_result
[2024-01-25 17:35:46,980] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:46,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:47,007] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:47,007] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:47,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014357575.1_ASM1435757v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:47,008] [INFO] Task started: Blastn
[2024-01-25 17:35:47,008] [INFO] Running command: blastn -query GCF_014357575.1_ASM1435757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5ba1a1c-7f32-4ee7-95b6-0271348cde63/dqc_reference/reference_markers_gtdb.fasta -out GCF_014357575.1_ASM1435757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:48,445] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:48,452] [INFO] Selected 10 target genomes.
[2024-01-25 17:35:48,452] [INFO] Target genome list was writen to GCF_014357575.1_ASM1435757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:48,458] [INFO] Task started: fastANI
[2024-01-25 17:35:48,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg282f04cd-98be-410b-886d-8be792e79fc5/GCF_014357575.1_ASM1435757v1_genomic.fna.gz --refList GCF_014357575.1_ASM1435757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014357575.1_ASM1435757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:04,637] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:04,644] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:04,645] [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_014357575.1	s__Pseudomonas_E foliumensis	100.0	1828	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	98.09	0.93	0.93	2	conclusive
GCF_002699985.1	s__Pseudomonas_E sp002699985	92.1557	1642	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.02	96.43	0.89	0.87	4	-
GCF_002158995.1	s__Pseudomonas_E caspiana	90.1426	1484	1842	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_900602065.1	s__Pseudomonas_E sp900602065	87.6222	1426	1842	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_900590755.1	s__Pseudomonas_E sp900590755	84.2424	1226	1842	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_900601905.1	s__Pseudomonas_E sp900601905	83.7662	1202	1842	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_000737245.1	s__Pseudomonas_E syringae_J	83.7622	1160	1842	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_000282475.1	s__Pseudomonas_E sp000282475	80.7218	749	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.83	0.83	2	-
GCF_004348895.1	s__Pseudomonas_E vancouverensis	80.715	770	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017980685.1	s__Pseudomonas_E iridis	80.7043	775	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.83	96.38	0.88	0.86	9	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:04,646] [INFO] GTDB search result was written to GCF_014357575.1_ASM1435757v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:04,647] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:04,650] [INFO] DFAST_QC result json was written to GCF_014357575.1_ASM1435757v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:04,650] [INFO] DFAST_QC completed!
[2024-01-25 17:36:04,650] [INFO] Total running time: 0h1m58s