[2024-01-25 19:56:35,747] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:35,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:35,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg34797e99-53fe-4021-9aeb-4495737b09ba/dqc_reference
[2024-01-25 19:56:36,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:36,880] [INFO] Task started: Prodigal
[2024-01-25 19:56:36,880] [INFO] Running command: gunzip -c /var/lib/cwl/stga110aea2-5c47-493c-8dff-4f8af17dbc69/GCF_014694385.1_ASM1469438v1_genomic.fna.gz | prodigal -d GCF_014694385.1_ASM1469438v1_genomic.fna/cds.fna -a GCF_014694385.1_ASM1469438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:54,522] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:54,522] [INFO] Task started: HMMsearch
[2024-01-25 19:56:54,522] [INFO] Running command: hmmsearch --tblout GCF_014694385.1_ASM1469438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34797e99-53fe-4021-9aeb-4495737b09ba/dqc_reference/reference_markers.hmm GCF_014694385.1_ASM1469438v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:54,799] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:54,800] [INFO] Found 6/6 markers.
[2024-01-25 19:56:54,848] [INFO] Query marker FASTA was written to GCF_014694385.1_ASM1469438v1_genomic.fna/markers.fasta
[2024-01-25 19:56:54,848] [INFO] Task started: Blastn
[2024-01-25 19:56:54,848] [INFO] Running command: blastn -query GCF_014694385.1_ASM1469438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34797e99-53fe-4021-9aeb-4495737b09ba/dqc_reference/reference_markers.fasta -out GCF_014694385.1_ASM1469438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:55,711] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:55,714] [INFO] Selected 23 target genomes.
[2024-01-25 19:56:55,714] [INFO] Target genome list was writen to GCF_014694385.1_ASM1469438v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:55,734] [INFO] Task started: fastANI
[2024-01-25 19:56:55,734] [INFO] Running command: fastANI --query /var/lib/cwl/stga110aea2-5c47-493c-8dff-4f8af17dbc69/GCF_014694385.1_ASM1469438v1_genomic.fna.gz --refList GCF_014694385.1_ASM1469438v1_genomic.fna/target_genomes.txt --output GCF_014694385.1_ASM1469438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:19,446] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:19,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34797e99-53fe-4021-9aeb-4495737b09ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:19,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34797e99-53fe-4021-9aeb-4495737b09ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:19,460] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:19,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:19,460] [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 typographi	strain=CA3A	GCA_014694385.1	2715964	2715964	type	True	100.0	1922	1927	95	conclusive
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	79.836	691	1927	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	79.7642	728	1927	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	79.6881	668	1927	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	79.5969	673	1927	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	79.5349	615	1927	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	79.5253	666	1927	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	79.5151	671	1927	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	79.5123	667	1927	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	79.5055	691	1927	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	79.4256	623	1927	95	below_threshold
Pseudomonas rhizosphaerae	strain=DSM 16299	GCA_000761155.1	216142	216142	type	True	79.372	631	1927	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	79.3448	600	1927	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	79.3325	668	1927	95	below_threshold
Pseudomonas massiliensis	strain=CB1	GCA_000826105.1	522492	522492	type	True	79.225	629	1927	95	below_threshold
Pseudomonas zanjanensis	strain=SWRI12	GCA_014268745.2	2745496	2745496	type	True	79.2215	595	1927	95	below_threshold
Pseudomonas bijieensis	strain=L22-9	GCA_013347965.1	2681983	2681983	type	True	79.0692	659	1927	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.9749	522	1927	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	78.7602	515	1927	95	below_threshold
Pseudomonas quercus	strain=hsmgli-8	GCA_012033695.1	2722792	2722792	type	True	78.6987	514	1927	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	78.6474	505	1927	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.6446	430	1927	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.1959	427	1927	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:19,463] [INFO] DFAST Taxonomy check result was written to GCF_014694385.1_ASM1469438v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:19,465] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:19,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:19,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34797e99-53fe-4021-9aeb-4495737b09ba/dqc_reference/checkm_data
[2024-01-25 19:57:19,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:19,528] [INFO] Task started: CheckM
[2024-01-25 19:57:19,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014694385.1_ASM1469438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014694385.1_ASM1469438v1_genomic.fna/checkm_input GCF_014694385.1_ASM1469438v1_genomic.fna/checkm_result
[2024-01-25 19:58:08,103] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:08,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:08,122] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:08,122] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:08,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014694385.1_ASM1469438v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:08,123] [INFO] Task started: Blastn
[2024-01-25 19:58:08,123] [INFO] Running command: blastn -query GCF_014694385.1_ASM1469438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34797e99-53fe-4021-9aeb-4495737b09ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_014694385.1_ASM1469438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:09,648] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:09,651] [INFO] Selected 28 target genomes.
[2024-01-25 19:58:09,651] [INFO] Target genome list was writen to GCF_014694385.1_ASM1469438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:09,677] [INFO] Task started: fastANI
[2024-01-25 19:58:09,677] [INFO] Running command: fastANI --query /var/lib/cwl/stga110aea2-5c47-493c-8dff-4f8af17dbc69/GCF_014694385.1_ASM1469438v1_genomic.fna.gz --refList GCF_014694385.1_ASM1469438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014694385.1_ASM1469438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:39,787] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:39,803] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:39,803] [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_014694385.1	s__Pseudomonas_E typographi	100.0	1922	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.61	99.56	0.95	0.95	3	conclusive
GCF_003097135.1	s__Pseudomonas_E sp003097135	80.3295	775	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	4	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	79.8315	692	1927	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_002806685.1	s__Pseudomonas_E qingdaonensis	79.7521	738	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
GCF_013374995.1	s__Pseudomonas_E eucalypticola	79.7449	726	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	99.03	0.96	0.96	2	-
GCA_000497835.1	s__Pseudomonas_E sp000497835	79.619	742	1927	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_000621225.1	s__Pseudomonas_E mosselii	79.5974	673	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	79.5844	617	1927	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_001642705.1	s__Pseudomonas_E sp001642705	79.5586	675	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_001941965.1	s__Pseudomonas_E putida_L	79.4758	687	1927	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_002025705.1	s__Pseudomonas_E putida_J	79.4718	655	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.29	96.26	0.90	0.90	5	-
GCF_001534745.1	s__Pseudomonas_E monteilii_A	79.3946	588	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.81	97.29	0.91	0.89	7	-
GCF_003671955.1	s__Pseudomonas_E hunanensis	79.3799	607	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_015680235.1	s__Pseudomonas_E guariconensis_A	79.3713	639	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.73	0.91	0.90	4	-
GCF_000746525.1	s__Pseudomonas_E alkylphenolica	79.3524	599	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.61	96.52	0.84	0.83	3	-
GCF_004357765.1	s__Pseudomonas_E putida_U	79.3491	616	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	-
GCF_000263855.1	s__Pseudomonas_E sp000263855	79.3412	734	1927	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_000319305.2	s__Pseudomonas_E putida_C	79.3289	668	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	97.35	0.88	0.88	2	-
GCF_004214895.1	s__Pseudomonas_E sp004214895	79.3187	651	1927	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_014268745.2	s__Pseudomonas_E sp014268745	79.2293	594	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.32	95.56	0.90	0.87	3	-
GCF_000931465.1	s__Pseudomonas_E sp000931465	79.2248	721	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.96	0.96	2	-
GCF_000826105.1	s__Pseudomonas_E massiliensis	79.2236	630	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013347965.1	s__Pseudomonas_E bijieensis	79.0579	660	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.40	95.64	0.93	0.88	7	-
GCF_003999415.1	s__Pseudomonas_E koreensis_E	78.8719	589	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_008801475.1	s__Pseudomonas_E moorei	78.7824	588	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012033695.1	s__Pseudomonas_E quercus	78.7023	513	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017589465.1	s__Pseudomonas sp017589465	78.5015	528	1927	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:39,804] [INFO] GTDB search result was written to GCF_014694385.1_ASM1469438v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:39,805] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:39,809] [INFO] DFAST_QC result json was written to GCF_014694385.1_ASM1469438v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:39,809] [INFO] DFAST_QC completed!
[2024-01-25 19:58:39,809] [INFO] Total running time: 0h2m4s