[2024-01-25 19:01:20,884] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:20,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:20,886] [INFO] DQC Reference Directory: /var/lib/cwl/stge569102e-e721-4f7a-bd99-56889ebbf910/dqc_reference
[2024-01-25 19:01:21,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:21,997] [INFO] Task started: Prodigal
[2024-01-25 19:01:21,997] [INFO] Running command: gunzip -c /var/lib/cwl/stg15d27e6b-e1db-43de-ba21-0d0bda3de322/GCF_002158995.1_ASM215899v1_genomic.fna.gz | prodigal -d GCF_002158995.1_ASM215899v1_genomic.fna/cds.fna -a GCF_002158995.1_ASM215899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:38,117] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:38,117] [INFO] Task started: HMMsearch
[2024-01-25 19:01:38,118] [INFO] Running command: hmmsearch --tblout GCF_002158995.1_ASM215899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge569102e-e721-4f7a-bd99-56889ebbf910/dqc_reference/reference_markers.hmm GCF_002158995.1_ASM215899v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:38,555] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:38,556] [INFO] Found 6/6 markers.
[2024-01-25 19:01:38,612] [INFO] Query marker FASTA was written to GCF_002158995.1_ASM215899v1_genomic.fna/markers.fasta
[2024-01-25 19:01:38,613] [INFO] Task started: Blastn
[2024-01-25 19:01:38,613] [INFO] Running command: blastn -query GCF_002158995.1_ASM215899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge569102e-e721-4f7a-bd99-56889ebbf910/dqc_reference/reference_markers.fasta -out GCF_002158995.1_ASM215899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:39,444] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:39,449] [INFO] Selected 34 target genomes.
[2024-01-25 19:01:39,449] [INFO] Target genome list was writen to GCF_002158995.1_ASM215899v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:39,469] [INFO] Task started: fastANI
[2024-01-25 19:01:39,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg15d27e6b-e1db-43de-ba21-0d0bda3de322/GCF_002158995.1_ASM215899v1_genomic.fna.gz --refList GCF_002158995.1_ASM215899v1_genomic.fna/target_genomes.txt --output GCF_002158995.1_ASM215899v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:17,111] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:17,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge569102e-e721-4f7a-bd99-56889ebbf910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:17,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge569102e-e721-4f7a-bd99-56889ebbf910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:17,131] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:02:17,131] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:02:17,131] [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	81.5029	1019	2009	95	below_threshold
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	81.4891	1023	2009	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	81.4867	1036	2009	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	81.4681	953	2009	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4303	GCA_001401395.1	251701	251701	pathovar	True	81.2317	949	2009	95	below_threshold
Pseudomonas cannabina	strain=ICMP 15200	GCA_001401375.1	86840	86840	pathovar	True	81.2043	923	2009	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP529	GCA_001400335.1	251701	251701	pathovar	True	81.1893	928	2009	95	below_threshold
Pseudomonas cannabina	strain=ICMP2823	GCA_001400175.1	86840	86840	type	True	81.1814	910	2009	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP2814	GCA_001401385.1	251701	251701	pathovar	True	81.1791	939	2009	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4116	GCA_001401405.1	251701	251701	pathovar	True	81.1318	964	2009	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	81.1303	1000	2009	95	below_threshold
Pseudomonas cannabina	strain=ICMP 2823	GCA_900100365.1	86840	86840	type	True	81.1154	963	2009	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP8903	GCA_001400595.1	251701	251701	pathovar	True	81.1075	946	2009	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	81.0922	1001	2009	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	80.7559	886	2009	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	80.7518	840	2009	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	80.7509	860	2009	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	80.7388	852	2009	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	80.629	865	2009	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	80.5933	870	2009	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	80.5826	838	2009	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	80.5684	858	2009	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	80.5222	836	2009	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_001983165.1	78544	78544	type	True	80.5163	763	2009	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	80.515	849	2009	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	80.5072	765	2009	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	80.4976	851	2009	95	below_threshold
Pseudomonas umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	80.4904	812	2009	95	below_threshold
Pseudomonas brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	80.4699	759	2009	95	below_threshold
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	80.453	768	2009	95	below_threshold
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	80.4359	766	2009	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	80.034	615	2009	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	79.9676	688	2009	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	77.9754	374	2009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:17,132] [INFO] DFAST Taxonomy check result was written to GCF_002158995.1_ASM215899v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:17,133] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:17,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:17,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge569102e-e721-4f7a-bd99-56889ebbf910/dqc_reference/checkm_data
[2024-01-25 19:02:17,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:17,193] [INFO] Task started: CheckM
[2024-01-25 19:02:17,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002158995.1_ASM215899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002158995.1_ASM215899v1_genomic.fna/checkm_input GCF_002158995.1_ASM215899v1_genomic.fna/checkm_result
[2024-01-25 19:03:04,461] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:04,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:04,479] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:04,479] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:04,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002158995.1_ASM215899v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:04,480] [INFO] Task started: Blastn
[2024-01-25 19:03:04,480] [INFO] Running command: blastn -query GCF_002158995.1_ASM215899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge569102e-e721-4f7a-bd99-56889ebbf910/dqc_reference/reference_markers_gtdb.fasta -out GCF_002158995.1_ASM215899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:05,812] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:05,815] [INFO] Selected 11 target genomes.
[2024-01-25 19:03:05,815] [INFO] Target genome list was writen to GCF_002158995.1_ASM215899v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:05,828] [INFO] Task started: fastANI
[2024-01-25 19:03:05,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg15d27e6b-e1db-43de-ba21-0d0bda3de322/GCF_002158995.1_ASM215899v1_genomic.fna.gz --refList GCF_002158995.1_ASM215899v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002158995.1_ASM215899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:23,786] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:23,793] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:23,793] [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_002158995.1	s__Pseudomonas_E caspiana	99.9999	2000	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014357575.1	s__Pseudomonas_E foliumensis	90.0471	1455	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	98.09	0.93	0.93	2	-
GCF_002699985.1	s__Pseudomonas_E sp002699985	88.9454	1608	2009	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_900602065.1	s__Pseudomonas_E sp900602065	87.5695	1596	2009	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	84.2414	1354	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900475325.1	s__Pseudomonas_E sp900475325	83.946	1307	2009	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	83.7956	1247	2009	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	83.7819	1254	2009	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_004364415.1	s__Pseudomonas_E mandelii_D	80.7825	882	2009	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_004348895.1	s__Pseudomonas_E vancouverensis	80.639	778	2009	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	80.6112	818	2009	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 19:03:23,796] [INFO] GTDB search result was written to GCF_002158995.1_ASM215899v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:23,796] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:23,800] [INFO] DFAST_QC result json was written to GCF_002158995.1_ASM215899v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:23,800] [INFO] DFAST_QC completed!
[2024-01-25 19:03:23,800] [INFO] Total running time: 0h2m3s