[2024-01-24 10:47:40,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg020e04ed-a722-4208-86ec-31a160faed2a/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd3db044-1e47-4e77-b571-9b445be2e2dc/GCF_019339365.1_ASM1933936v1_genomic.fna.gz | prodigal -d GCF_019339365.1_ASM1933936v1_genomic.fna/cds.fna -a GCF_019339365.1_ASM1933936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:58,268] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:58,269] [INFO] Task started: HMMsearch
[2024-01-24 10:47:58,269] [INFO] Running command: hmmsearch --tblout GCF_019339365.1_ASM1933936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg020e04ed-a722-4208-86ec-31a160faed2a/dqc_reference/reference_markers.hmm GCF_019339365.1_ASM1933936v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:58,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:58,579] [INFO] Found 6/6 markers.
[2024-01-24 10:47:58,638] [INFO] Query marker FASTA was written to GCF_019339365.1_ASM1933936v1_genomic.fna/markers.fasta
[2024-01-24 10:47:58,639] [INFO] Task started: Blastn
[2024-01-24 10:47:58,639] [INFO] Running command: blastn -query GCF_019339365.1_ASM1933936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg020e04ed-a722-4208-86ec-31a160faed2a/dqc_reference/reference_markers.fasta -out GCF_019339365.1_ASM1933936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:59,416] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:59,420] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:59,420] [INFO] Target genome list was writen to GCF_019339365.1_ASM1933936v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:59,431] [INFO] Task started: fastANI
[2024-01-24 10:47:59,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd3db044-1e47-4e77-b571-9b445be2e2dc/GCF_019339365.1_ASM1933936v1_genomic.fna.gz --refList GCF_019339365.1_ASM1933936v1_genomic.fna/target_genomes.txt --output GCF_019339365.1_ASM1933936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:21,711] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:21,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg020e04ed-a722-4208-86ec-31a160faed2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:21,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg020e04ed-a722-4208-86ec-31a160faed2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:21,733] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:21,733] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:21,734] [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 coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	88.8594	1322	1787	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	82.0974	628	1787	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	81.8321	574	1787	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	81.6568	615	1787	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	81.2231	590	1787	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	81.0816	571	1787	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.8665	557	1787	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	80.8638	408	1787	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	80.8634	413	1787	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	80.7962	418	1787	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.78	388	1787	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.6936	563	1787	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	80.647	454	1787	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.5718	382	1787	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.517	367	1787	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.5103	389	1787	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	80.4003	500	1787	95	below_threshold
Vibrio alginolyticus	strain=NBRC 15630	GCA_000467145.1	663	663	type	True	80.3449	389	1787	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	80.2905	501	1787	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	80.22	422	1787	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.1432	386	1787	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000152485.1	150340	150340	suspected-type	True	79.9852	359	1787	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	79.953	433	1787	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	79.4124	368	1787	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	79.0855	328	1787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:21,735] [INFO] DFAST Taxonomy check result was written to GCF_019339365.1_ASM1933936v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:21,736] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:21,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:21,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg020e04ed-a722-4208-86ec-31a160faed2a/dqc_reference/checkm_data
[2024-01-24 10:48:21,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:21,787] [INFO] Task started: CheckM
[2024-01-24 10:48:21,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019339365.1_ASM1933936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019339365.1_ASM1933936v1_genomic.fna/checkm_input GCF_019339365.1_ASM1933936v1_genomic.fna/checkm_result
[2024-01-24 10:49:06,100] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:06,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:06,125] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:06,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:06,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019339365.1_ASM1933936v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:06,126] [INFO] Task started: Blastn
[2024-01-24 10:49:06,127] [INFO] Running command: blastn -query GCF_019339365.1_ASM1933936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg020e04ed-a722-4208-86ec-31a160faed2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019339365.1_ASM1933936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:07,336] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:07,341] [INFO] Selected 18 target genomes.
[2024-01-24 10:49:07,341] [INFO] Target genome list was writen to GCF_019339365.1_ASM1933936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:07,367] [INFO] Task started: fastANI
[2024-01-24 10:49:07,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd3db044-1e47-4e77-b571-9b445be2e2dc/GCF_019339365.1_ASM1933936v1_genomic.fna.gz --refList GCF_019339365.1_ASM1933936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019339365.1_ASM1933936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:25,283] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:25,298] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:25,298] [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_000967495.1	s__Vibrio neptunius	96.7531	1518	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	conclusive
GCF_000176135.1	s__Vibrio coralliilyticus	88.8731	1320	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_013113835.1	s__Vibrio sp013113835	88.5095	1272	1787	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	82.0928	626	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_001695575.1	s__Vibrio europaeus	81.6989	614	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_001399455.2	s__Vibrio bivalvicida	81.2055	591	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_006124995.1	s__Vibrio sp006124995	80.9385	505	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189275.1	s__Vibrio sinaloensis_B	80.9365	519	1787	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	80.932	540	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808535.1	s__Vibrio sinaloensis	80.9175	535	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_003970385.1	s__Vibrio aquaticus	80.8904	554	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004551525.1	s__Vibrio ouci	80.8857	569	1787	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	80.8773	554	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_001274785.1	s__Vibrio hepatarius	80.8167	497	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_009938205.1	s__Vibrio panuliri	80.4007	386	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_001591105.1	s__Vibrio nereis	80.3105	499	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCA_001048675.1	s__Vibrio diabolicus	80.2049	397	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000740015.1	s__Vibrio diazotrophicus	79.0996	327	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:25,299] [INFO] GTDB search result was written to GCF_019339365.1_ASM1933936v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:25,300] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:25,305] [INFO] DFAST_QC result json was written to GCF_019339365.1_ASM1933936v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:25,305] [INFO] DFAST_QC completed!
[2024-01-24 10:49:25,305] [INFO] Total running time: 0h1m44s