[2024-01-24 15:27:41,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,308] [INFO] DQC Reference Directory: /var/lib/cwl/stgf79e202f-3438-4c1a-ac68-569260dcfc43/dqc_reference
[2024-01-24 15:27:43,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,886] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,887] [INFO] Running command: gunzip -c /var/lib/cwl/stg11aca2dd-fdb5-4397-8fe8-ba0defc542d8/GCF_019670125.1_ASM1967012v1_genomic.fna.gz | prodigal -d GCF_019670125.1_ASM1967012v1_genomic.fna/cds.fna -a GCF_019670125.1_ASM1967012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:54,394] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:54,394] [INFO] Task started: HMMsearch
[2024-01-24 15:27:54,394] [INFO] Running command: hmmsearch --tblout GCF_019670125.1_ASM1967012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf79e202f-3438-4c1a-ac68-569260dcfc43/dqc_reference/reference_markers.hmm GCF_019670125.1_ASM1967012v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:54,700] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:54,702] [INFO] Found 6/6 markers.
[2024-01-24 15:27:54,743] [INFO] Query marker FASTA was written to GCF_019670125.1_ASM1967012v1_genomic.fna/markers.fasta
[2024-01-24 15:27:54,744] [INFO] Task started: Blastn
[2024-01-24 15:27:54,744] [INFO] Running command: blastn -query GCF_019670125.1_ASM1967012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf79e202f-3438-4c1a-ac68-569260dcfc43/dqc_reference/reference_markers.fasta -out GCF_019670125.1_ASM1967012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:55,515] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:55,518] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:55,518] [INFO] Target genome list was writen to GCF_019670125.1_ASM1967012v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:55,522] [INFO] Task started: fastANI
[2024-01-24 15:27:55,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg11aca2dd-fdb5-4397-8fe8-ba0defc542d8/GCF_019670125.1_ASM1967012v1_genomic.fna.gz --refList GCF_019670125.1_ASM1967012v1_genomic.fna/target_genomes.txt --output GCF_019670125.1_ASM1967012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:05,985] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:05,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf79e202f-3438-4c1a-ac68-569260dcfc43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:05,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf79e202f-3438-4c1a-ac68-569260dcfc43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:05,998] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:05,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:05,999] [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
Agarivorans aestuarii	strain=KCTC 32543	GCA_019670125.1	1563703	1563703	type	True	100.0	1562	1562	95	conclusive
Agarivorans albus	strain=JCM 21469	GCA_019670105.1	182262	182262	type	True	92.5707	1357	1562	95	below_threshold
Agarivorans albus	strain=MKT 106	GCA_000414175.1	182262	182262	type	True	92.5326	1326	1562	95	below_threshold
Agarivorans litoreus	strain=NBRC 110444	GCA_019649015.1	1510455	1510455	type	True	90.6227	1282	1562	95	below_threshold
Agarivorans gilvus	strain=WH0801	GCA_001420915.1	680279	680279	type	True	80.4309	561	1562	95	below_threshold
Agarivorans gilvus	strain=CGMCC 1.10131	GCA_014636215.1	680279	680279	type	True	80.0439	560	1562	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.7125	80	1562	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	79.5164	69	1562	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	78.8855	87	1562	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	78.5269	92	1562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:06,004] [INFO] DFAST Taxonomy check result was written to GCF_019670125.1_ASM1967012v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:06,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:06,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:06,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf79e202f-3438-4c1a-ac68-569260dcfc43/dqc_reference/checkm_data
[2024-01-24 15:28:06,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:06,051] [INFO] Task started: CheckM
[2024-01-24 15:28:06,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019670125.1_ASM1967012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019670125.1_ASM1967012v1_genomic.fna/checkm_input GCF_019670125.1_ASM1967012v1_genomic.fna/checkm_result
[2024-01-24 15:28:40,932] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:40,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:40,952] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:40,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:40,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019670125.1_ASM1967012v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:40,953] [INFO] Task started: Blastn
[2024-01-24 15:28:40,954] [INFO] Running command: blastn -query GCF_019670125.1_ASM1967012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf79e202f-3438-4c1a-ac68-569260dcfc43/dqc_reference/reference_markers_gtdb.fasta -out GCF_019670125.1_ASM1967012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:42,088] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:42,092] [INFO] Selected 10 target genomes.
[2024-01-24 15:28:42,093] [INFO] Target genome list was writen to GCF_019670125.1_ASM1967012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:42,105] [INFO] Task started: fastANI
[2024-01-24 15:28:42,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg11aca2dd-fdb5-4397-8fe8-ba0defc542d8/GCF_019670125.1_ASM1967012v1_genomic.fna.gz --refList GCF_019670125.1_ASM1967012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019670125.1_ASM1967012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:51,369] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:51,380] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:28:51,381] [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_000414175.1	s__Agarivorans albus	92.5326	1326	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	96.96	96.96	0.93	0.93	2	-
GCF_900537085.1	s__Agarivorans sp900537085	90.0289	1308	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405585.1	s__Agarivorans sp005405585	82.267	900	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420915.1	s__Agarivorans gilvus	80.4344	562	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002076895.1	s__Cognaticolwellia beringensis	78.66	67	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429485.1	s__Aliagarivorans marinus	77.7906	148	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Aliagarivorans	95.1281	N/A	N/A	N/A	N/A	1	-
GCF_000429505.1	s__Aliagarivorans taiwanensis	77.769	146	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Aliagarivorans	95.1281	N/A	N/A	N/A	N/A	1	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	77.311	62	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_016464335.1	s__Aliivibrio fischeri	76.9873	63	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.1568	96.45	95.48	0.88	0.84	60	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:51,383] [INFO] GTDB search result was written to GCF_019670125.1_ASM1967012v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:51,384] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:51,390] [INFO] DFAST_QC result json was written to GCF_019670125.1_ASM1967012v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:51,390] [INFO] DFAST_QC completed!
[2024-01-24 15:28:51,391] [INFO] Total running time: 0h1m10s