[2024-01-24 13:19:01,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,195] [INFO] DQC Reference Directory: /var/lib/cwl/stgebdfeb4c-f00d-4ab3-88b5-8c30d837721b/dqc_reference
[2024-01-24 13:19:02,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,527] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d4de9db-d227-46f3-a8c7-3465410e6b7e/GCF_000354175.2_ASM35417v2_genomic.fna.gz | prodigal -d GCF_000354175.2_ASM35417v2_genomic.fna/cds.fna -a GCF_000354175.2_ASM35417v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:15,769] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:15,770] [INFO] Task started: HMMsearch
[2024-01-24 13:19:15,770] [INFO] Running command: hmmsearch --tblout GCF_000354175.2_ASM35417v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebdfeb4c-f00d-4ab3-88b5-8c30d837721b/dqc_reference/reference_markers.hmm GCF_000354175.2_ASM35417v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:16,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:16,137] [INFO] Found 6/6 markers.
[2024-01-24 13:19:16,192] [INFO] Query marker FASTA was written to GCF_000354175.2_ASM35417v2_genomic.fna/markers.fasta
[2024-01-24 13:19:16,192] [INFO] Task started: Blastn
[2024-01-24 13:19:16,192] [INFO] Running command: blastn -query GCF_000354175.2_ASM35417v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgebdfeb4c-f00d-4ab3-88b5-8c30d837721b/dqc_reference/reference_markers.fasta -out GCF_000354175.2_ASM35417v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:17,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:17,039] [INFO] Selected 12 target genomes.
[2024-01-24 13:19:17,039] [INFO] Target genome list was writen to GCF_000354175.2_ASM35417v2_genomic.fna/target_genomes.txt
[2024-01-24 13:19:17,045] [INFO] Task started: fastANI
[2024-01-24 13:19:17,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d4de9db-d227-46f3-a8c7-3465410e6b7e/GCF_000354175.2_ASM35417v2_genomic.fna.gz --refList GCF_000354175.2_ASM35417v2_genomic.fna/target_genomes.txt --output GCF_000354175.2_ASM35417v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:31,845] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:31,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebdfeb4c-f00d-4ab3-88b5-8c30d837721b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:31,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebdfeb4c-f00d-4ab3-88b5-8c30d837721b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:31,856] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:19:31,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:31,856] [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 alginolyticus	strain=ATCC 17749	GCA_000354175.2	663	663	type	True	100.0	1712	1715	95	conclusive
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	99.9894	1708	1715	95	conclusive
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	99.9809	1690	1715	95	conclusive
Vibrio alginolyticus	strain=NBRC 15630	GCA_000467145.1	663	663	type	True	99.9757	1640	1715	95	conclusive
Vibrio antiquarius	strain=EX25	GCA_000024825.1	150340	150340	suspected-type	True	92.6568	1483	1715	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000152485.1	150340	150340	suspected-type	True	92.3277	1370	1715	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	86.2762	1242	1715	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	82.9876	912	1715	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.8632	460	1715	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.656	400	1715	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.6503	481	1715	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.6101	396	1715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:31,858] [INFO] DFAST Taxonomy check result was written to GCF_000354175.2_ASM35417v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:31,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:31,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:31,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebdfeb4c-f00d-4ab3-88b5-8c30d837721b/dqc_reference/checkm_data
[2024-01-24 13:19:31,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:31,914] [INFO] Task started: CheckM
[2024-01-24 13:19:31,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000354175.2_ASM35417v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000354175.2_ASM35417v2_genomic.fna/checkm_input GCF_000354175.2_ASM35417v2_genomic.fna/checkm_result
[2024-01-24 13:20:16,845] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:16,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:16,885] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:16,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:16,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000354175.2_ASM35417v2_genomic.fna/markers.fasta)
[2024-01-24 13:20:16,887] [INFO] Task started: Blastn
[2024-01-24 13:20:16,887] [INFO] Running command: blastn -query GCF_000354175.2_ASM35417v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgebdfeb4c-f00d-4ab3-88b5-8c30d837721b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000354175.2_ASM35417v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:18,090] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:18,093] [INFO] Selected 13 target genomes.
[2024-01-24 13:20:18,093] [INFO] Target genome list was writen to GCF_000354175.2_ASM35417v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:18,101] [INFO] Task started: fastANI
[2024-01-24 13:20:18,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d4de9db-d227-46f3-a8c7-3465410e6b7e/GCF_000354175.2_ASM35417v2_genomic.fna.gz --refList GCF_000354175.2_ASM35417v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000354175.2_ASM35417v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:33,079] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:33,095] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:33,096] [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_000354175.2	s__Vibrio alginolyticus	100.0	1715	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	conclusive
GCA_001048675.1	s__Vibrio diabolicus	92.5727	1481	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_900460535.1	s__Vibrio parahaemolyticus	86.2686	1244	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCF_000817815.1	s__Vibrio owensii	85.167	1048	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_002563795.1	s__Vibrio sp002563795	84.8244	1019	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163755.1	s__Vibrio campbellii	84.4647	1044	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000400365.1	s__Vibrio jasicida	84.3409	1048	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_001591145.1	s__Vibrio harveyi	84.2572	1037	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_002741985.1	s__Vibrio rotiferianus	84.068	947	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000417905.1	s__Vibrio natriegens	82.7731	894	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
GCA_018222805.1	s__Vibrio sp018222805	82.4405	797	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000830505.1	s__Vibrio mytili	81.8293	735	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274785.1	s__Vibrio hepatarius	80.9458	470	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:33,098] [INFO] GTDB search result was written to GCF_000354175.2_ASM35417v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:33,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:33,102] [INFO] DFAST_QC result json was written to GCF_000354175.2_ASM35417v2_genomic.fna/dqc_result.json
[2024-01-24 13:20:33,102] [INFO] DFAST_QC completed!
[2024-01-24 13:20:33,102] [INFO] Total running time: 0h1m32s