[2024-01-24 13:12:39,106] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:39,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:39,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c0ca5b5-7c7a-4d25-b2ba-ba27c1e96bcb/dqc_reference
[2024-01-24 13:12:40,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,485] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg7692b60a-b145-45af-9237-e8875cffdccd/GCF_002741985.1_ASM274198v1_genomic.fna.gz | prodigal -d GCF_002741985.1_ASM274198v1_genomic.fna/cds.fna -a GCF_002741985.1_ASM274198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:53,863] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:53,864] [INFO] Task started: HMMsearch
[2024-01-24 13:12:53,864] [INFO] Running command: hmmsearch --tblout GCF_002741985.1_ASM274198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c0ca5b5-7c7a-4d25-b2ba-ba27c1e96bcb/dqc_reference/reference_markers.hmm GCF_002741985.1_ASM274198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:54,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:54,334] [INFO] Found 6/6 markers.
[2024-01-24 13:12:54,379] [INFO] Query marker FASTA was written to GCF_002741985.1_ASM274198v1_genomic.fna/markers.fasta
[2024-01-24 13:12:54,379] [INFO] Task started: Blastn
[2024-01-24 13:12:54,379] [INFO] Running command: blastn -query GCF_002741985.1_ASM274198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c0ca5b5-7c7a-4d25-b2ba-ba27c1e96bcb/dqc_reference/reference_markers.fasta -out GCF_002741985.1_ASM274198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:55,259] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:55,263] [INFO] Selected 15 target genomes.
[2024-01-24 13:12:55,264] [INFO] Target genome list was writen to GCF_002741985.1_ASM274198v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:55,275] [INFO] Task started: fastANI
[2024-01-24 13:12:55,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg7692b60a-b145-45af-9237-e8875cffdccd/GCF_002741985.1_ASM274198v1_genomic.fna.gz --refList GCF_002741985.1_ASM274198v1_genomic.fna/target_genomes.txt --output GCF_002741985.1_ASM274198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:12,918] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:12,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c0ca5b5-7c7a-4d25-b2ba-ba27c1e96bcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:12,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c0ca5b5-7c7a-4d25-b2ba-ba27c1e96bcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:12,932] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:12,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:12,932] [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 rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	100.0	1734	1737	95	conclusive
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	88.9844	1140	1737	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	88.9488	1266	1737	95	below_threshold
Vibrio harveyi	strain=ATCC 14126	GCA_001263135.1	669	669	type	True	88.7321	1222	1737	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	88.6304	1244	1737	95	below_threshold
Vibrio harveyi	strain=NCTC12970	GCA_900460165.1	669	669	type	True	88.6262	1282	1737	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	87.4638	1235	1737	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	87.4271	1254	1737	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000024825.1	150340	150340	suspected-type	True	83.6197	954	1737	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000152485.1	150340	150340	suspected-type	True	83.0825	879	1737	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	82.2435	796	1737	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.7723	409	1737	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.7212	411	1737	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.6859	497	1737	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.6719	485	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:12,934] [INFO] DFAST Taxonomy check result was written to GCF_002741985.1_ASM274198v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:12,935] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:12,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:12,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c0ca5b5-7c7a-4d25-b2ba-ba27c1e96bcb/dqc_reference/checkm_data
[2024-01-24 13:13:12,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:12,991] [INFO] Task started: CheckM
[2024-01-24 13:13:12,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002741985.1_ASM274198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002741985.1_ASM274198v1_genomic.fna/checkm_input GCF_002741985.1_ASM274198v1_genomic.fna/checkm_result
[2024-01-24 13:13:55,792] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:55,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:55,815] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:55,815] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:55,816] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002741985.1_ASM274198v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:55,816] [INFO] Task started: Blastn
[2024-01-24 13:13:55,816] [INFO] Running command: blastn -query GCF_002741985.1_ASM274198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c0ca5b5-7c7a-4d25-b2ba-ba27c1e96bcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002741985.1_ASM274198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:56,996] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:56,999] [INFO] Selected 8 target genomes.
[2024-01-24 13:13:56,999] [INFO] Target genome list was writen to GCF_002741985.1_ASM274198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:57,015] [INFO] Task started: fastANI
[2024-01-24 13:13:57,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg7692b60a-b145-45af-9237-e8875cffdccd/GCF_002741985.1_ASM274198v1_genomic.fna.gz --refList GCF_002741985.1_ASM274198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002741985.1_ASM274198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:07,594] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:07,610] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:07,611] [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_002741985.1	s__Vibrio rotiferianus	100.0	1734	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	conclusive
GCF_002163755.1	s__Vibrio campbellii	89.0398	1192	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000817815.1	s__Vibrio owensii	88.9393	1267	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_001591145.1	s__Vibrio harveyi	88.6486	1242	1737	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	87.6913	1282	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002906655.1	s__Vibrio hyugaensis	87.436	1254	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_000171815.1	s__Vibrio sp000171815	84.6202	827	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000354175.2	s__Vibrio alginolyticus	84.1884	958	1737	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:07,613] [INFO] GTDB search result was written to GCF_002741985.1_ASM274198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:07,613] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:07,619] [INFO] DFAST_QC result json was written to GCF_002741985.1_ASM274198v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:07,620] [INFO] DFAST_QC completed!
[2024-01-24 13:14:07,620] [INFO] Total running time: 0h1m29s