[2024-01-24 14:13:01,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,383] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd91e39d-682e-4823-9299-55e669be0838/dqc_reference
[2024-01-24 14:13:02,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,604] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f9ef2f4-eb00-4b71-938d-4abe831c8209/GCF_000429505.1_ASM42950v1_genomic.fna.gz | prodigal -d GCF_000429505.1_ASM42950v1_genomic.fna/cds.fna -a GCF_000429505.1_ASM42950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:14,553] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:14,553] [INFO] Task started: HMMsearch
[2024-01-24 14:13:14,553] [INFO] Running command: hmmsearch --tblout GCF_000429505.1_ASM42950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd91e39d-682e-4823-9299-55e669be0838/dqc_reference/reference_markers.hmm GCF_000429505.1_ASM42950v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:14,834] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:14,835] [INFO] Found 6/6 markers.
[2024-01-24 14:13:14,878] [INFO] Query marker FASTA was written to GCF_000429505.1_ASM42950v1_genomic.fna/markers.fasta
[2024-01-24 14:13:14,878] [INFO] Task started: Blastn
[2024-01-24 14:13:14,878] [INFO] Running command: blastn -query GCF_000429505.1_ASM42950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd91e39d-682e-4823-9299-55e669be0838/dqc_reference/reference_markers.fasta -out GCF_000429505.1_ASM42950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:15,815] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:15,820] [INFO] Selected 13 target genomes.
[2024-01-24 14:13:15,821] [INFO] Target genome list was writen to GCF_000429505.1_ASM42950v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:15,830] [INFO] Task started: fastANI
[2024-01-24 14:13:15,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f9ef2f4-eb00-4b71-938d-4abe831c8209/GCF_000429505.1_ASM42950v1_genomic.fna.gz --refList GCF_000429505.1_ASM42950v1_genomic.fna/target_genomes.txt --output GCF_000429505.1_ASM42950v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:26,246] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:26,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd91e39d-682e-4823-9299-55e669be0838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:26,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd91e39d-682e-4823-9299-55e669be0838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:26,255] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:26,255] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:13:26,255] [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
Aliagarivorans taiwanensis	strain=DSM 22990	GCA_000429505.1	561966	561966	type	True	100.0	1429	1434	95	inconclusive
Aliagarivorans marinus	strain=DSM 23064	GCA_000429485.1	561965	561965	type	True	95.0235	1243	1434	95	inconclusive
Agarivorans albus	strain=JCM 21469	GCA_019670105.1	182262	182262	type	True	77.7018	154	1434	95	below_threshold
Agarivorans albus	strain=MKT 106	GCA_000414175.1	182262	182262	type	True	77.6419	150	1434	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	77.4284	83	1434	95	below_threshold
Agarivorans aestuarii	strain=KCTC 32543	GCA_019670125.1	1563703	1563703	type	True	77.4102	167	1434	95	below_threshold
Agarivorans litoreus	strain=NBRC 110444	GCA_019649015.1	1510455	1510455	type	True	77.373	157	1434	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	76.5272	56	1434	95	below_threshold
Aeromonas australiensis	strain=CECT 8023	GCA_000819725.1	1114880	1114880	type	True	76.3397	94	1434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:26,257] [INFO] DFAST Taxonomy check result was written to GCF_000429505.1_ASM42950v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:26,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:26,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:26,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd91e39d-682e-4823-9299-55e669be0838/dqc_reference/checkm_data
[2024-01-24 14:13:26,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:26,307] [INFO] Task started: CheckM
[2024-01-24 14:13:26,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429505.1_ASM42950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429505.1_ASM42950v1_genomic.fna/checkm_input GCF_000429505.1_ASM42950v1_genomic.fna/checkm_result
[2024-01-24 14:14:05,819] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:05,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:05,843] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:05,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:05,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429505.1_ASM42950v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:05,844] [INFO] Task started: Blastn
[2024-01-24 14:14:05,844] [INFO] Running command: blastn -query GCF_000429505.1_ASM42950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd91e39d-682e-4823-9299-55e669be0838/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429505.1_ASM42950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:07,218] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:07,221] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:07,221] [INFO] Target genome list was writen to GCF_000429505.1_ASM42950v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:07,237] [INFO] Task started: fastANI
[2024-01-24 14:14:07,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f9ef2f4-eb00-4b71-938d-4abe831c8209/GCF_000429505.1_ASM42950v1_genomic.fna.gz --refList GCF_000429505.1_ASM42950v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429505.1_ASM42950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:19,478] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:19,493] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:19,493] [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_000429505.1	s__Aliagarivorans taiwanensis	100.0	1429	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Aliagarivorans	95.1281	N/A	N/A	N/A	N/A	1	conclusive
GCF_000429485.1	s__Aliagarivorans marinus	95.0212	1244	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Aliagarivorans	95.1281	N/A	N/A	N/A	N/A	1	-
GCF_900537085.1	s__Agarivorans sp900537085	77.751	149	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414175.1	s__Agarivorans albus	77.6	152	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	96.96	96.96	0.93	0.93	2	-
GCF_005405585.1	s__Agarivorans sp005405585	77.5318	138	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176515.1	s__Enterovibrio hollisae	77.4971	81	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.40	99.22	0.97	0.96	10	-
GCA_000755425.1	s__Vibrio maritimus_A	77.0015	72	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353085.1	s__Shewanella corallii	76.9911	81	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000755385.1	s__Vibrio maritimus_B	76.6234	80	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.88	95.88	0.85	0.85	2	-
GCF_003812745.1	s__Serratia sp003812745	76.3507	74	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.8367	N/A	N/A	N/A	N/A	1	-
GCF_000819725.1	s__Aeromonas australiensis	76.3397	94	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187905.1	s__Pantoea sp001187905	76.2817	68	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:19,495] [INFO] GTDB search result was written to GCF_000429505.1_ASM42950v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:19,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:19,499] [INFO] DFAST_QC result json was written to GCF_000429505.1_ASM42950v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:19,499] [INFO] DFAST_QC completed!
[2024-01-24 14:14:19,499] [INFO] Total running time: 0h1m18s