[2024-01-24 13:55:27,891] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:27,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:27,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg86a1c068-676b-4413-99a8-49ae0d5a05c7/dqc_reference
[2024-01-24 13:55:29,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:29,135] [INFO] Task started: Prodigal
[2024-01-24 13:55:29,136] [INFO] Running command: gunzip -c /var/lib/cwl/stg8efd8ac6-8899-4c72-8f33-26722564a4d7/GCF_000176235.1_ASM17623v1_genomic.fna.gz | prodigal -d GCF_000176235.1_ASM17623v1_genomic.fna/cds.fna -a GCF_000176235.1_ASM17623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:39,923] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:39,924] [INFO] Task started: HMMsearch
[2024-01-24 13:55:39,924] [INFO] Running command: hmmsearch --tblout GCF_000176235.1_ASM17623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86a1c068-676b-4413-99a8-49ae0d5a05c7/dqc_reference/reference_markers.hmm GCF_000176235.1_ASM17623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:40,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:40,165] [INFO] Found 6/6 markers.
[2024-01-24 13:55:40,205] [INFO] Query marker FASTA was written to GCF_000176235.1_ASM17623v1_genomic.fna/markers.fasta
[2024-01-24 13:55:40,206] [INFO] Task started: Blastn
[2024-01-24 13:55:40,206] [INFO] Running command: blastn -query GCF_000176235.1_ASM17623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86a1c068-676b-4413-99a8-49ae0d5a05c7/dqc_reference/reference_markers.fasta -out GCF_000176235.1_ASM17623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:40,959] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:40,963] [INFO] Selected 13 target genomes.
[2024-01-24 13:55:40,963] [INFO] Target genome list was writen to GCF_000176235.1_ASM17623v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:40,979] [INFO] Task started: fastANI
[2024-01-24 13:55:40,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg8efd8ac6-8899-4c72-8f33-26722564a4d7/GCF_000176235.1_ASM17623v1_genomic.fna.gz --refList GCF_000176235.1_ASM17623v1_genomic.fna/target_genomes.txt --output GCF_000176235.1_ASM17623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:54,261] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:54,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86a1c068-676b-4413-99a8-49ae0d5a05c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:54,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86a1c068-676b-4413-99a8-49ae0d5a05c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:54,273] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:55:54,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:54,274] [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
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	100.0	1564	1564	95	conclusive
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	99.9572	1504	1564	95	conclusive
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	83.8269	944	1564	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	82.4127	823	1564	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	82.3577	782	1564	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	82.3129	787	1564	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	82.2189	832	1564	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.8466	504	1564	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	80.8377	494	1564	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.837	444	1564	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.7467	485	1564	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.3807	464	1564	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	80.0831	415	1564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:54,275] [INFO] DFAST Taxonomy check result was written to GCF_000176235.1_ASM17623v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:54,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:54,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:54,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86a1c068-676b-4413-99a8-49ae0d5a05c7/dqc_reference/checkm_data
[2024-01-24 13:55:54,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:54,322] [INFO] Task started: CheckM
[2024-01-24 13:55:54,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000176235.1_ASM17623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000176235.1_ASM17623v1_genomic.fna/checkm_input GCF_000176235.1_ASM17623v1_genomic.fna/checkm_result
[2024-01-24 13:56:30,597] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:30,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:30,620] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:30,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:30,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000176235.1_ASM17623v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:30,621] [INFO] Task started: Blastn
[2024-01-24 13:56:30,621] [INFO] Running command: blastn -query GCF_000176235.1_ASM17623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86a1c068-676b-4413-99a8-49ae0d5a05c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000176235.1_ASM17623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:31,741] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:31,744] [INFO] Selected 12 target genomes.
[2024-01-24 13:56:31,744] [INFO] Target genome list was writen to GCF_000176235.1_ASM17623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:31,761] [INFO] Task started: fastANI
[2024-01-24 13:56:31,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg8efd8ac6-8899-4c72-8f33-26722564a4d7/GCF_000176235.1_ASM17623v1_genomic.fna.gz --refList GCF_000176235.1_ASM17623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000176235.1_ASM17623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:44,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:44,318] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:44,318] [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_000176235.1	s__Vibrio orientalis	100.0	1564	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004551525.1	s__Vibrio ouci	89.9287	1313	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970385.1	s__Vibrio aquaticus	83.8179	943	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114545.1	s__Vibrio sp013114545	82.9023	826	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189255.1	s__Vibrio brasiliensis	82.4846	753	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772105.1	s__Vibrio tubiashii	82.3991	825	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_001399455.2	s__Vibrio bivalvicida	82.344	784	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_001695575.1	s__Vibrio europaeus	82.2451	829	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000808535.1	s__Vibrio sinaloensis	82.1185	667	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_006124995.1	s__Vibrio sp006124995	82.0376	707	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811315.1	s__Vibrio atypicus	81.9357	729	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000967495.1	s__Vibrio neptunius	80.7212	537	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:44,320] [INFO] GTDB search result was written to GCF_000176235.1_ASM17623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:44,320] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:44,325] [INFO] DFAST_QC result json was written to GCF_000176235.1_ASM17623v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:44,326] [INFO] DFAST_QC completed!
[2024-01-24 13:56:44,326] [INFO] Total running time: 0h1m16s