[2024-01-25 18:13:20,519] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg4444408f-a53b-4037-8321-3f9ca80b2d95/dqc_reference
[2024-01-25 18:13:21,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,694] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,694] [INFO] Running command: gunzip -c /var/lib/cwl/stgad0b22b5-83bd-4fff-bc02-2d58bf5bd876/GCF_003751625.1_ASM375162v1_genomic.fna.gz | prodigal -d GCF_003751625.1_ASM375162v1_genomic.fna/cds.fna -a GCF_003751625.1_ASM375162v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:33,392] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:33,392] [INFO] Task started: HMMsearch
[2024-01-25 18:13:33,392] [INFO] Running command: hmmsearch --tblout GCF_003751625.1_ASM375162v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4444408f-a53b-4037-8321-3f9ca80b2d95/dqc_reference/reference_markers.hmm GCF_003751625.1_ASM375162v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:33,675] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:33,676] [INFO] Found 6/6 markers.
[2024-01-25 18:13:33,711] [INFO] Query marker FASTA was written to GCF_003751625.1_ASM375162v1_genomic.fna/markers.fasta
[2024-01-25 18:13:33,711] [INFO] Task started: Blastn
[2024-01-25 18:13:33,711] [INFO] Running command: blastn -query GCF_003751625.1_ASM375162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4444408f-a53b-4037-8321-3f9ca80b2d95/dqc_reference/reference_markers.fasta -out GCF_003751625.1_ASM375162v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:34,532] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:34,534] [INFO] Selected 19 target genomes.
[2024-01-25 18:13:34,534] [INFO] Target genome list was writen to GCF_003751625.1_ASM375162v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:34,577] [INFO] Task started: fastANI
[2024-01-25 18:13:34,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgad0b22b5-83bd-4fff-bc02-2d58bf5bd876/GCF_003751625.1_ASM375162v1_genomic.fna.gz --refList GCF_003751625.1_ASM375162v1_genomic.fna/target_genomes.txt --output GCF_003751625.1_ASM375162v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:48,690] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:48,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4444408f-a53b-4037-8321-3f9ca80b2d95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:48,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4444408f-a53b-4037-8321-3f9ca80b2d95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:48,704] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:48,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:48,705] [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
Gallaecimonas pentaromativorans	strain=DSM 21945	GCA_003751625.1	584787	584787	type	True	100.0	1388	1390	95	conclusive
Gallaecimonas xiamenensis	strain=3-C-1	GCA_000299915.1	1207039	1207039	type	True	83.3509	878	1390	95	below_threshold
Gallaecimonas mangrovi	strain=HK-28	GCA_003367375.1	2291597	2291597	type	True	80.5427	728	1390	95	below_threshold
Zobellella taiwanensis	strain=JCM 13381	GCA_003012795.1	347535	347535	type	True	77.4795	202	1390	95	below_threshold
Aeromonas bivalvium	strain=CECT 7113	GCA_000819765.1	440079	440079	type	True	77.2694	182	1390	95	below_threshold
Aeromonas taiwanensis	strain=LMG 24683	GCA_000699185.1	633417	633417	type	True	77.1521	182	1390	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	76.999	198	1390	95	below_threshold
Aeromonas aquatica	strain=AE235	GCA_000764655.1	558964	558964	type	True	76.9151	175	1390	95	below_threshold
Aeromonas enteropelogenes	strain=FDAARGOS_1509	GCA_020097315.1	29489	29489	type	True	76.8717	184	1390	95	below_threshold
Aeromonas enteropelogenes	strain=CECT 4487	GCA_000819845.1	29489	29489	type	True	76.8022	180	1390	95	below_threshold
Plesiomonas shigelloides	strain=NCTC10360	GCA_900087055.1	703	703	type	True	76.6712	81	1390	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	76.5477	161	1390	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.4978	81	1390	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.4972	81	1390	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.4917	147	1390	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	76.4456	148	1390	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.3491	119	1390	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.3072	135	1390	95	below_threshold
Ferrimonas senticii	strain=DSM 18821	GCA_000422665.1	394566	394566	type	True	76.1787	83	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:48,706] [INFO] DFAST Taxonomy check result was written to GCF_003751625.1_ASM375162v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:48,706] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:48,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:48,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4444408f-a53b-4037-8321-3f9ca80b2d95/dqc_reference/checkm_data
[2024-01-25 18:13:48,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:48,749] [INFO] Task started: CheckM
[2024-01-25 18:13:48,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003751625.1_ASM375162v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003751625.1_ASM375162v1_genomic.fna/checkm_input GCF_003751625.1_ASM375162v1_genomic.fna/checkm_result
[2024-01-25 18:14:24,321] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:24,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:24,344] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:24,345] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:24,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003751625.1_ASM375162v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:24,346] [INFO] Task started: Blastn
[2024-01-25 18:14:24,346] [INFO] Running command: blastn -query GCF_003751625.1_ASM375162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4444408f-a53b-4037-8321-3f9ca80b2d95/dqc_reference/reference_markers_gtdb.fasta -out GCF_003751625.1_ASM375162v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:25,755] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:25,758] [INFO] Selected 17 target genomes.
[2024-01-25 18:14:25,758] [INFO] Target genome list was writen to GCF_003751625.1_ASM375162v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:25,777] [INFO] Task started: fastANI
[2024-01-25 18:14:25,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgad0b22b5-83bd-4fff-bc02-2d58bf5bd876/GCF_003751625.1_ASM375162v1_genomic.fna.gz --refList GCF_003751625.1_ASM375162v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003751625.1_ASM375162v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:38,834] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:38,844] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:38,845] [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_003751625.1	s__Gallaecimonas pentaromativorans	100.0	1388	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	98.58	98.58	0.94	0.94	2	conclusive
GCF_000299915.1	s__Gallaecimonas xiamenensis	83.3811	875	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367375.1	s__Gallaecimonas mangrovi	80.5685	726	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Gallaecimonadaceae;g__Gallaecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012795.1	s__Zobellella_D taiwanensis	77.4802	202	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819765.1	s__Aeromonas bivalvium	77.2694	182	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.28	98.27	0.92	0.92	5	-
GCF_000243075.1	s__Oceanimonas sp000243075	77.2134	225	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637545.1	s__Aeromonas encheleia	77.0848	175	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_003049725.1	s__Oceanimonas marisflavi	77.0276	197	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764655.1	s__Aeromonas aquatica	76.9151	175	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819845.1	s__Aeromonas enteropelogenes	76.8038	180	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_900087055.1	s__Plesiomonas shigelloides	76.6712	81	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Plesiomonas	95.0	97.46	97.09	0.91	0.86	29	-
GCF_005116715.1	s__Ferrimonas sp005116715	76.5598	160	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018596335.1	s__Shewanella sp018596335	76.5062	146	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	76.4732	147	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009189165.1	s__Pseudomonas sp009189165	76.4177	141	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	76.318	120	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422665.1	s__Ferrimonas senticii	76.1481	84	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:38,846] [INFO] GTDB search result was written to GCF_003751625.1_ASM375162v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:38,847] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:38,850] [INFO] DFAST_QC result json was written to GCF_003751625.1_ASM375162v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:38,850] [INFO] DFAST_QC completed!
[2024-01-25 18:14:38,850] [INFO] Total running time: 0h1m18s