[2024-01-24 11:42:20,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg91c17d92-7a96-4be5-95e8-1cd91439f3d0/dqc_reference
[2024-01-24 11:42:24,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ce4d744-6c65-48ad-b00a-7042a40dc6db/GCF_016881005.1_ASM1688100v1_genomic.fna.gz | prodigal -d GCF_016881005.1_ASM1688100v1_genomic.fna/cds.fna -a GCF_016881005.1_ASM1688100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:44,517] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:44,517] [INFO] Task started: HMMsearch
[2024-01-24 11:42:44,517] [INFO] Running command: hmmsearch --tblout GCF_016881005.1_ASM1688100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91c17d92-7a96-4be5-95e8-1cd91439f3d0/dqc_reference/reference_markers.hmm GCF_016881005.1_ASM1688100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:44,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:44,837] [INFO] Found 6/6 markers.
[2024-01-24 11:42:44,887] [INFO] Query marker FASTA was written to GCF_016881005.1_ASM1688100v1_genomic.fna/markers.fasta
[2024-01-24 11:42:44,887] [INFO] Task started: Blastn
[2024-01-24 11:42:44,887] [INFO] Running command: blastn -query GCF_016881005.1_ASM1688100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91c17d92-7a96-4be5-95e8-1cd91439f3d0/dqc_reference/reference_markers.fasta -out GCF_016881005.1_ASM1688100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:45,744] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:45,748] [INFO] Selected 18 target genomes.
[2024-01-24 11:42:45,748] [INFO] Target genome list was writen to GCF_016881005.1_ASM1688100v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:45,756] [INFO] Task started: fastANI
[2024-01-24 11:42:45,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ce4d744-6c65-48ad-b00a-7042a40dc6db/GCF_016881005.1_ASM1688100v1_genomic.fna.gz --refList GCF_016881005.1_ASM1688100v1_genomic.fna/target_genomes.txt --output GCF_016881005.1_ASM1688100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:08,421] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:08,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91c17d92-7a96-4be5-95e8-1cd91439f3d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:08,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91c17d92-7a96-4be5-95e8-1cd91439f3d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:08,439] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:08,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:08,439] [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 arcuscaelestis	strain=P66	GCA_016881005.1	2710591	2710591	type	True	100.0	2054	2056	95	conclusive
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	86.1868	1390	2056	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	85.031	1309	2056	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	83.0563	904	2056	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	82.53	906	2056	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	82.3469	1053	2056	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	82.2032	1083	2056	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	81.9713	1004	2056	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	81.8292	1039	2056	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	81.8289	1085	2056	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	81.5443	1048	2056	95	below_threshold
Pseudomonas guariconensis	strain=LMG 27394	GCA_900102675.1	1288410	1288410	suspected-type	True	81.407	979	2056	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	81.2129	956	2056	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	81.1971	969	2056	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	81.1796	977	2056	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	80.9511	799	2056	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	80.8127	937	2056	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	80.8113	826	2056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:08,441] [INFO] DFAST Taxonomy check result was written to GCF_016881005.1_ASM1688100v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:08,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:08,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:08,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91c17d92-7a96-4be5-95e8-1cd91439f3d0/dqc_reference/checkm_data
[2024-01-24 11:43:08,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:08,501] [INFO] Task started: CheckM
[2024-01-24 11:43:08,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016881005.1_ASM1688100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016881005.1_ASM1688100v1_genomic.fna/checkm_input GCF_016881005.1_ASM1688100v1_genomic.fna/checkm_result
[2024-01-24 11:44:05,784] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:05,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:05,806] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:05,806] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:05,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016881005.1_ASM1688100v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:05,807] [INFO] Task started: Blastn
[2024-01-24 11:44:05,807] [INFO] Running command: blastn -query GCF_016881005.1_ASM1688100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91c17d92-7a96-4be5-95e8-1cd91439f3d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_016881005.1_ASM1688100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:07,249] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:07,253] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:07,254] [INFO] Target genome list was writen to GCF_016881005.1_ASM1688100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:07,267] [INFO] Task started: fastANI
[2024-01-24 11:44:07,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ce4d744-6c65-48ad-b00a-7042a40dc6db/GCF_016881005.1_ASM1688100v1_genomic.fna.gz --refList GCF_016881005.1_ASM1688100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016881005.1_ASM1688100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:28,205] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:28,229] [INFO] Found 15 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:44:28,230] [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_016865545.1	s__Pseudomonas_E sp016865545	99.3424	1667	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.73	0.87	0.86	3	inconclusive
GCF_004803755.1	s__Pseudomonas_E sp004803755	95.0656	1693	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000746525.1	s__Pseudomonas_E alkylphenolica	86.1827	1391	2056	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_003024385.1	s__Pseudomonas_E sp003024385	86.0834	1270	2056	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_000955815.1	s__Pseudomonas_E sp000955815	85.2175	1352	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.49	99.49	0.96	0.96	2	-
GCF_000425805.1	s__Pseudomonas_E vranovensis	85.0328	1309	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.71	99.71	0.93	0.93	2	-
GCF_016009175.1	s__Pseudomonas_E alkylphenolica_B	84.9496	1321	2056	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_900497695.1	s__Pseudomonas_E wadenswilerensis	84.9461	1311	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.26	0.95	0.95	2	-
GCF_018417635.1	s__Pseudomonas_E sp900101695	84.775	1290	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.49	97.27	0.95	0.94	5	-
GCF_004353925.1	s__Pseudomonas_E sp004353925	84.5934	1322	2056	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	81.7481	1078	2056	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_013386115.1	s__Pseudomonas_E gingeri_B	80.8759	887	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	98.43	0.94	0.92	9	-
GCF_002113595.1	s__Pseudomonas_E sp002113595	80.8114	923	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	96.42	0.97	0.93	16	-
GCF_001269655.1	s__Pseudomonas_E thivervalensis	80.8114	827	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	98.81	0.96	0.93	6	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	78.7128	411	2056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:28,231] [INFO] GTDB search result was written to GCF_016881005.1_ASM1688100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:28,231] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:28,235] [INFO] DFAST_QC result json was written to GCF_016881005.1_ASM1688100v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:28,235] [INFO] DFAST_QC completed!
[2024-01-24 11:44:28,236] [INFO] Total running time: 0h2m8s