[2024-01-24 13:40:55,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ae038ff-ba13-4484-a9d1-240093340f51/dqc_reference
[2024-01-24 13:40:56,433] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,434] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,434] [INFO] Running command: gunzip -c /var/lib/cwl/stg585fae2f-287c-4706-98f6-a6c99978dfa7/GCF_003544875.1_ASM354487v1_genomic.fna.gz | prodigal -d GCF_003544875.1_ASM354487v1_genomic.fna/cds.fna -a GCF_003544875.1_ASM354487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:07,299] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:07,299] [INFO] Task started: HMMsearch
[2024-01-24 13:41:07,299] [INFO] Running command: hmmsearch --tblout GCF_003544875.1_ASM354487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ae038ff-ba13-4484-a9d1-240093340f51/dqc_reference/reference_markers.hmm GCF_003544875.1_ASM354487v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:07,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:07,590] [INFO] Found 6/6 markers.
[2024-01-24 13:41:07,627] [INFO] Query marker FASTA was written to GCF_003544875.1_ASM354487v1_genomic.fna/markers.fasta
[2024-01-24 13:41:07,628] [INFO] Task started: Blastn
[2024-01-24 13:41:07,628] [INFO] Running command: blastn -query GCF_003544875.1_ASM354487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ae038ff-ba13-4484-a9d1-240093340f51/dqc_reference/reference_markers.fasta -out GCF_003544875.1_ASM354487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:08,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:08,398] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:08,398] [INFO] Target genome list was writen to GCF_003544875.1_ASM354487v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:08,404] [INFO] Task started: fastANI
[2024-01-24 13:41:08,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg585fae2f-287c-4706-98f6-a6c99978dfa7/GCF_003544875.1_ASM354487v1_genomic.fna.gz --refList GCF_003544875.1_ASM354487v1_genomic.fna/target_genomes.txt --output GCF_003544875.1_ASM354487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:26,318] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:26,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ae038ff-ba13-4484-a9d1-240093340f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:26,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ae038ff-ba13-4484-a9d1-240093340f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:26,329] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:26,330] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:26,330] [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 owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	85.1653	1017	1635	95	below_threshold
Vibrio harveyi	strain=FDAARGOS_109	GCA_001471575.2	669	669	type	True	84.9949	1062	1635	95	below_threshold
Vibrio harveyi	strain=NCTC12970	GCA_900460165.1	669	669	type	True	84.9933	1060	1635	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	84.8549	1056	1635	95	below_threshold
Vibrio harveyi	strain=ATCC 14126	GCA_001263135.1	669	669	type	True	84.8018	1004	1635	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	84.7138	1016	1635	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	84.7136	1040	1635	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	84.7038	915	1635	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	84.4794	988	1635	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	82.9385	897	1635	95	below_threshold
Vibrio parahaemolyticus		GCA_001558495.2	670	670	type	True	82.9026	906	1635	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	82.6398	867	1635	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	81.9109	753	1635	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	81.0627	408	1635	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.8293	458	1635	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.7932	391	1635	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	80.1077	440	1635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:26,331] [INFO] DFAST Taxonomy check result was written to GCF_003544875.1_ASM354487v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:26,332] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:26,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:26,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ae038ff-ba13-4484-a9d1-240093340f51/dqc_reference/checkm_data
[2024-01-24 13:41:26,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:26,380] [INFO] Task started: CheckM
[2024-01-24 13:41:26,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003544875.1_ASM354487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003544875.1_ASM354487v1_genomic.fna/checkm_input GCF_003544875.1_ASM354487v1_genomic.fna/checkm_result
[2024-01-24 13:42:00,670] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:00,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:00,685] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:00,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:00,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003544875.1_ASM354487v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:00,685] [INFO] Task started: Blastn
[2024-01-24 13:42:00,685] [INFO] Running command: blastn -query GCF_003544875.1_ASM354487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ae038ff-ba13-4484-a9d1-240093340f51/dqc_reference/reference_markers_gtdb.fasta -out GCF_003544875.1_ASM354487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:01,851] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:01,854] [INFO] Selected 10 target genomes.
[2024-01-24 13:42:01,854] [INFO] Target genome list was writen to GCF_003544875.1_ASM354487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:01,859] [INFO] Task started: fastANI
[2024-01-24 13:42:01,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg585fae2f-287c-4706-98f6-a6c99978dfa7/GCF_003544875.1_ASM354487v1_genomic.fna.gz --refList GCF_003544875.1_ASM354487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003544875.1_ASM354487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:14,125] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:14,133] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:14,133] [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_003544875.1	s__Vibrio alfacsensis	100.0	1634	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.49	96.49	0.89	0.89	2	conclusive
GCF_000817815.1	s__Vibrio owensii	85.1515	1019	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_002163755.1	s__Vibrio campbellii	84.8806	983	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_002906655.1	s__Vibrio hyugaensis	84.8488	1057	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_001591145.1	s__Vibrio harveyi	84.6912	1018	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_000400365.1	s__Vibrio jasicida	84.6769	1029	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002741985.1	s__Vibrio rotiferianus	84.4975	987	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_002608565.1	s__Vibrio sp002608565	84.0452	937	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.42	99.42	0.94	0.94	2	-
GCF_900460535.1	s__Vibrio parahaemolyticus	82.9224	900	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCA_001048675.1	s__Vibrio diabolicus	82.7807	839	1635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:14,134] [INFO] GTDB search result was written to GCF_003544875.1_ASM354487v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:14,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:14,138] [INFO] DFAST_QC result json was written to GCF_003544875.1_ASM354487v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:14,138] [INFO] DFAST_QC completed!
[2024-01-24 13:42:14,138] [INFO] Total running time: 0h1m19s