[2024-01-25 19:35:50,956] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:50,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:50,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd690fc7-e68b-4783-9ecb-9abab128b6c1/dqc_reference
[2024-01-25 19:35:52,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,189] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,189] [INFO] Running command: gunzip -c /var/lib/cwl/stgca3a46df-755a-4646-a175-56f1540fe91d/GCF_000830505.1_ASM83050v1_genomic.fna.gz | prodigal -d GCF_000830505.1_ASM83050v1_genomic.fna/cds.fna -a GCF_000830505.1_ASM83050v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:02,016] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:02,016] [INFO] Task started: HMMsearch
[2024-01-25 19:36:02,016] [INFO] Running command: hmmsearch --tblout GCF_000830505.1_ASM83050v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd690fc7-e68b-4783-9ecb-9abab128b6c1/dqc_reference/reference_markers.hmm GCF_000830505.1_ASM83050v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:02,293] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:02,294] [INFO] Found 6/6 markers.
[2024-01-25 19:36:02,340] [INFO] Query marker FASTA was written to GCF_000830505.1_ASM83050v1_genomic.fna/markers.fasta
[2024-01-25 19:36:02,340] [INFO] Task started: Blastn
[2024-01-25 19:36:02,340] [INFO] Running command: blastn -query GCF_000830505.1_ASM83050v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd690fc7-e68b-4783-9ecb-9abab128b6c1/dqc_reference/reference_markers.fasta -out GCF_000830505.1_ASM83050v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:03,100] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:03,103] [INFO] Selected 15 target genomes.
[2024-01-25 19:36:03,104] [INFO] Target genome list was writen to GCF_000830505.1_ASM83050v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:03,108] [INFO] Task started: fastANI
[2024-01-25 19:36:03,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgca3a46df-755a-4646-a175-56f1540fe91d/GCF_000830505.1_ASM83050v1_genomic.fna.gz --refList GCF_000830505.1_ASM83050v1_genomic.fna/target_genomes.txt --output GCF_000830505.1_ASM83050v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:16,384] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:16,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd690fc7-e68b-4783-9ecb-9abab128b6c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:16,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd690fc7-e68b-4783-9ecb-9abab128b6c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:16,397] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:36:16,397] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:36:16,397] [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 natriegens	strain=CCUG 16371	GCA_001680045.1	691	691	type	True	81.9135	778	1497	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	81.7215	737	1497	95	below_threshold
Vibrio natriegens	strain=ATCC 14048	GCA_000417905.1	691	691	type	True	81.7169	770	1497	95	below_threshold
Vibrio natriegens	strain=DSM 759	GCA_000438785.2	691	691	type	True	81.7122	752	1497	95	below_threshold
Vibrio alginolyticus	strain=ATCC 17749	GCA_000354175.2	663	663	type	True	81.7092	747	1497	95	below_threshold
Vibrio alginolyticus	strain=NBRC 15630	GCA_000467145.1	663	663	type	True	81.7085	726	1497	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	81.7074	715	1497	95	below_threshold
Vibrio natriegens	strain=ATCC 14048	GCA_001680025.1	691	691	type	True	81.705	799	1497	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	81.6665	801	1497	95	below_threshold
Vibrio natriegens	strain=NBRC 15636	GCA_001591085.1	691	691	type	True	81.6431	793	1497	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000152485.1	150340	150340	suspected-type	True	81.4834	672	1497	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.4159	364	1497	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	78.9779	371	1497	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	78.887	352	1497	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.512	318	1497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:16,400] [INFO] DFAST Taxonomy check result was written to GCF_000830505.1_ASM83050v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:16,400] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:16,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:16,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd690fc7-e68b-4783-9ecb-9abab128b6c1/dqc_reference/checkm_data
[2024-01-25 19:36:16,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:16,450] [INFO] Task started: CheckM
[2024-01-25 19:36:16,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000830505.1_ASM83050v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000830505.1_ASM83050v1_genomic.fna/checkm_input GCF_000830505.1_ASM83050v1_genomic.fna/checkm_result
[2024-01-25 19:36:48,450] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:48,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:48,480] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:48,481] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:48,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000830505.1_ASM83050v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:48,481] [INFO] Task started: Blastn
[2024-01-25 19:36:48,481] [INFO] Running command: blastn -query GCF_000830505.1_ASM83050v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd690fc7-e68b-4783-9ecb-9abab128b6c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000830505.1_ASM83050v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:49,610] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:49,613] [INFO] Selected 10 target genomes.
[2024-01-25 19:36:49,613] [INFO] Target genome list was writen to GCF_000830505.1_ASM83050v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:49,622] [INFO] Task started: fastANI
[2024-01-25 19:36:49,622] [INFO] Running command: fastANI --query /var/lib/cwl/stgca3a46df-755a-4646-a175-56f1540fe91d/GCF_000830505.1_ASM83050v1_genomic.fna.gz --refList GCF_000830505.1_ASM83050v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000830505.1_ASM83050v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:59,644] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:59,651] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:59,651] [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_000830505.1	s__Vibrio mytili	100.0	1495	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001048675.1	s__Vibrio diabolicus	81.9815	750	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000417905.1	s__Vibrio natriegens	81.723	769	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
GCF_000354175.2	s__Vibrio alginolyticus	81.7005	748	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_900460535.1	s__Vibrio parahaemolyticus	81.6766	762	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCA_018223135.1	s__Vibrio sp018223135	81.5509	735	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905175385.1	s__Vibrio sp903986855	81.5315	727	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
GCA_018222805.1	s__Vibrio sp018222805	81.2258	711	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563795.1	s__Vibrio sp002563795	81.1074	689	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400365.1	s__Vibrio jasicida	81.0352	683	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:59,653] [INFO] GTDB search result was written to GCF_000830505.1_ASM83050v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:59,654] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:59,656] [INFO] DFAST_QC result json was written to GCF_000830505.1_ASM83050v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:59,656] [INFO] DFAST_QC completed!
[2024-01-25 19:36:59,657] [INFO] Total running time: 0h1m9s