[2024-01-24 12:36:56,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:56,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:56,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg57df27a2-610d-4ddf-ae32-d0ae9ca468e2/dqc_reference
[2024-01-24 12:36:58,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:58,263] [INFO] Task started: Prodigal
[2024-01-24 12:36:58,264] [INFO] Running command: gunzip -c /var/lib/cwl/stg686bd96e-d471-4761-906c-eb3e8f59b89d/GCF_014268785.2_ASM1426878v2_genomic.fna.gz | prodigal -d GCF_014268785.2_ASM1426878v2_genomic.fna/cds.fna -a GCF_014268785.2_ASM1426878v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:13,642] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:13,643] [INFO] Task started: HMMsearch
[2024-01-24 12:37:13,643] [INFO] Running command: hmmsearch --tblout GCF_014268785.2_ASM1426878v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57df27a2-610d-4ddf-ae32-d0ae9ca468e2/dqc_reference/reference_markers.hmm GCF_014268785.2_ASM1426878v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:13,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:13,977] [INFO] Found 6/6 markers.
[2024-01-24 12:37:14,018] [INFO] Query marker FASTA was written to GCF_014268785.2_ASM1426878v2_genomic.fna/markers.fasta
[2024-01-24 12:37:14,019] [INFO] Task started: Blastn
[2024-01-24 12:37:14,019] [INFO] Running command: blastn -query GCF_014268785.2_ASM1426878v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg57df27a2-610d-4ddf-ae32-d0ae9ca468e2/dqc_reference/reference_markers.fasta -out GCF_014268785.2_ASM1426878v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:15,111] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:15,115] [INFO] Selected 19 target genomes.
[2024-01-24 12:37:15,116] [INFO] Target genome list was writen to GCF_014268785.2_ASM1426878v2_genomic.fna/target_genomes.txt
[2024-01-24 12:37:15,131] [INFO] Task started: fastANI
[2024-01-24 12:37:15,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg686bd96e-d471-4761-906c-eb3e8f59b89d/GCF_014268785.2_ASM1426878v2_genomic.fna.gz --refList GCF_014268785.2_ASM1426878v2_genomic.fna/target_genomes.txt --output GCF_014268785.2_ASM1426878v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:38,225] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:38,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57df27a2-610d-4ddf-ae32-d0ae9ca468e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:38,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57df27a2-610d-4ddf-ae32-d0ae9ca468e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:38,240] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:38,240] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:38,240] [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 faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	84.9712	1110	1579	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	84.9567	1045	1579	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	84.6299	1071	1579	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	84.6258	1061	1579	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	84.5676	1119	1579	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	84.5331	1113	1579	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	84.4787	1128	1579	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	84.335	1080	1579	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	84.3184	1032	1579	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	84.2253	1107	1579	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	84.197	1004	1579	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	84.1642	1042	1579	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	84.1497	1107	1579	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	84.1482	1076	1579	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	84.1331	1094	1579	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	84.0451	1113	1579	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	84.0165	1114	1579	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	83.9904	1130	1579	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	83.9875	1095	1579	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:38,243] [INFO] DFAST Taxonomy check result was written to GCF_014268785.2_ASM1426878v2_genomic.fna/tc_result.tsv
[2024-01-24 12:37:38,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:38,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:38,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57df27a2-610d-4ddf-ae32-d0ae9ca468e2/dqc_reference/checkm_data
[2024-01-24 12:37:38,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:38,293] [INFO] Task started: CheckM
[2024-01-24 12:37:38,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268785.2_ASM1426878v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268785.2_ASM1426878v2_genomic.fna/checkm_input GCF_014268785.2_ASM1426878v2_genomic.fna/checkm_result
[2024-01-24 12:38:23,893] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:23,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:23,915] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:23,915] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:23,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268785.2_ASM1426878v2_genomic.fna/markers.fasta)
[2024-01-24 12:38:23,916] [INFO] Task started: Blastn
[2024-01-24 12:38:23,916] [INFO] Running command: blastn -query GCF_014268785.2_ASM1426878v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg57df27a2-610d-4ddf-ae32-d0ae9ca468e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268785.2_ASM1426878v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:25,857] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:25,863] [INFO] Selected 17 target genomes.
[2024-01-24 12:38:25,863] [INFO] Target genome list was writen to GCF_014268785.2_ASM1426878v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:25,877] [INFO] Task started: fastANI
[2024-01-24 12:38:25,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg686bd96e-d471-4761-906c-eb3e8f59b89d/GCF_014268785.2_ASM1426878v2_genomic.fna.gz --refList GCF_014268785.2_ASM1426878v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268785.2_ASM1426878v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:48,516] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:48,536] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:48,537] [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_002843585.1	s__Pseudomonas_E sp002843585	97.2491	1423	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	97.16	0.92	0.88	9	conclusive
GCF_900536025.1	s__Pseudomonas_E reidholzensis	86.1741	1206	1579	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_017875955.1	s__Pseudomonas_E sp017875955	85.4848	1176	1579	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_014268815.2	s__Pseudomonas_E sp014268815	85.1742	1200	1579	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_003231305.1	s__Pseudomonas_E sichuanensis	84.6811	1055	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	84.6244	1070	1579	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_003097235.1	s__Pseudomonas_E sp003097235	84.5334	1106	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_015354575.1	s__Pseudomonas_E sp015354575	84.4384	1071	1579	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_003205295.1	s__Pseudomonas_E mosselii_B	84.4082	1061	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_004519305.1	s__Pseudomonas_E sp004519305	84.3832	1019	1579	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_000282535.1	s__Pseudomonas_E sp000282535	84.3821	970	1579	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_001320245.1	s__Pseudomonas_E sp001320245	84.2126	1074	1579	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_016658545.1	s__Pseudomonas_E sp016658545	84.2044	1057	1579	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_000731675.1	s__Pseudomonas_E capeferrum	84.1951	1108	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	-
GCF_002736125.1	s__Pseudomonas_E putida_M	84.1453	1101	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.25	0.91	0.90	8	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	84.0811	1066	1579	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_002356095.1	s__Pseudomonas_E putida_H	83.7551	1115	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.82	98.35	0.91	0.82	20	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:48,541] [INFO] GTDB search result was written to GCF_014268785.2_ASM1426878v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:48,542] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:48,545] [INFO] DFAST_QC result json was written to GCF_014268785.2_ASM1426878v2_genomic.fna/dqc_result.json
[2024-01-24 12:38:48,546] [INFO] DFAST_QC completed!
[2024-01-24 12:38:48,546] [INFO] Total running time: 0h1m52s