[2024-01-24 15:26:04,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,906] [INFO] DQC Reference Directory: /var/lib/cwl/stgf14007ce-fd69-4da1-aa9a-f005d64dae20/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,024] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg55bec0d7-e797-40e6-a433-59b871a64b4c/GCF_003182095.1_ASM318209v1_genomic.fna.gz | prodigal -d GCF_003182095.1_ASM318209v1_genomic.fna/cds.fna -a GCF_003182095.1_ASM318209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:19,383] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:19,383] [INFO] Task started: HMMsearch
[2024-01-24 15:26:19,384] [INFO] Running command: hmmsearch --tblout GCF_003182095.1_ASM318209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf14007ce-fd69-4da1-aa9a-f005d64dae20/dqc_reference/reference_markers.hmm GCF_003182095.1_ASM318209v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:19,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:19,703] [INFO] Found 6/6 markers.
[2024-01-24 15:26:19,744] [INFO] Query marker FASTA was written to GCF_003182095.1_ASM318209v1_genomic.fna/markers.fasta
[2024-01-24 15:26:19,745] [INFO] Task started: Blastn
[2024-01-24 15:26:19,745] [INFO] Running command: blastn -query GCF_003182095.1_ASM318209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf14007ce-fd69-4da1-aa9a-f005d64dae20/dqc_reference/reference_markers.fasta -out GCF_003182095.1_ASM318209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:20,730] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:20,734] [INFO] Selected 27 target genomes.
[2024-01-24 15:26:20,734] [INFO] Target genome list was writen to GCF_003182095.1_ASM318209v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:20,746] [INFO] Task started: fastANI
[2024-01-24 15:26:20,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg55bec0d7-e797-40e6-a433-59b871a64b4c/GCF_003182095.1_ASM318209v1_genomic.fna.gz --refList GCF_003182095.1_ASM318209v1_genomic.fna/target_genomes.txt --output GCF_003182095.1_ASM318209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:40,254] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:40,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf14007ce-fd69-4da1-aa9a-f005d64dae20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:40,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf14007ce-fd69-4da1-aa9a-f005d64dae20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:40,282] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:40,282] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:40,282] [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
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	100.0	1418	1419	95	conclusive
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	80.1008	668	1419	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.2306	315	1419	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.8957	158	1419	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.789	217	1419	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	76.7804	255	1419	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.7152	316	1419	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.6817	210	1419	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	76.6274	290	1419	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.6184	169	1419	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.5809	259	1419	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.5546	263	1419	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.5432	228	1419	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.5383	118	1419	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	76.5252	165	1419	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.5024	163	1419	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	76.4186	187	1419	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	76.4098	158	1419	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.3957	327	1419	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	76.3482	297	1419	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	76.3296	311	1419	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.3169	188	1419	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	76.2976	189	1419	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.2307	173	1419	95	below_threshold
Acidihalobacter ferrooxydans	strain=V8	GCA_001975725.1	1765967	1765967	type	True	76.2001	152	1419	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	76.0252	115	1419	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.9261	260	1419	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:40,284] [INFO] DFAST Taxonomy check result was written to GCF_003182095.1_ASM318209v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:40,285] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:40,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:40,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf14007ce-fd69-4da1-aa9a-f005d64dae20/dqc_reference/checkm_data
[2024-01-24 15:26:40,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:40,334] [INFO] Task started: CheckM
[2024-01-24 15:26:40,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182095.1_ASM318209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182095.1_ASM318209v1_genomic.fna/checkm_input GCF_003182095.1_ASM318209v1_genomic.fna/checkm_result
[2024-01-24 15:27:22,711] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:22,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:22,736] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:22,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:22,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182095.1_ASM318209v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:22,737] [INFO] Task started: Blastn
[2024-01-24 15:27:22,737] [INFO] Running command: blastn -query GCF_003182095.1_ASM318209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf14007ce-fd69-4da1-aa9a-f005d64dae20/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182095.1_ASM318209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:24,693] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:24,698] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:24,698] [INFO] Target genome list was writen to GCF_003182095.1_ASM318209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:24,712] [INFO] Task started: fastANI
[2024-01-24 15:27:24,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg55bec0d7-e797-40e6-a433-59b871a64b4c/GCF_003182095.1_ASM318209v1_genomic.fna.gz --refList GCF_003182095.1_ASM318209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182095.1_ASM318209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:36,370] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:36,391] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:36,391] [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_003182095.1	s__Plasticicumulans acidivorans	100.0	1418	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018240295.1	s__Plasticicumulans sp003962905	80.5884	699	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	80.105	667	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	77.1255	379	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.0945	204	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.9578	227	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	76.8888	321	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCA_003989065.1	s__RXIW01 sp003989065	76.7454	188	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	76.7301	122	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.6914	208	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699715.1	s__Competibacter sp016699715	76.6146	175	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695245.1	s__REEE01 sp007695245	76.3737	173	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__REEE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262135.1	s__Contendobacter sp018262135	76.2975	120	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Contendobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241525.1	s__SZAS-83 sp018241525	76.2043	289	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	76.1878	307	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106025.1	s__Methylococcus sp016106025	76.1658	102	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004168015.1	s__Methylotetracoccus sp004168015	75.9275	93	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylotetracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:36,393] [INFO] GTDB search result was written to GCF_003182095.1_ASM318209v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:36,393] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:36,398] [INFO] DFAST_QC result json was written to GCF_003182095.1_ASM318209v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:36,398] [INFO] DFAST_QC completed!
[2024-01-24 15:27:36,398] [INFO] Total running time: 0h1m31s