[2024-01-24 11:34:36,882] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:36,884] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:36,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6a197b2-85b6-4803-82ae-dae529ae94fe/dqc_reference
[2024-01-24 11:34:39,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:39,642] [INFO] Task started: Prodigal
[2024-01-24 11:34:39,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg85017b12-fb6f-4847-af0c-434a6cdebceb/GCF_002811245.1_ASM281124v1_genomic.fna.gz | prodigal -d GCF_002811245.1_ASM281124v1_genomic.fna/cds.fna -a GCF_002811245.1_ASM281124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:48,271] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:48,271] [INFO] Task started: HMMsearch
[2024-01-24 11:34:48,271] [INFO] Running command: hmmsearch --tblout GCF_002811245.1_ASM281124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6a197b2-85b6-4803-82ae-dae529ae94fe/dqc_reference/reference_markers.hmm GCF_002811245.1_ASM281124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:48,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:48,582] [INFO] Found 6/6 markers.
[2024-01-24 11:34:48,625] [INFO] Query marker FASTA was written to GCF_002811245.1_ASM281124v1_genomic.fna/markers.fasta
[2024-01-24 11:34:48,625] [INFO] Task started: Blastn
[2024-01-24 11:34:48,625] [INFO] Running command: blastn -query GCF_002811245.1_ASM281124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6a197b2-85b6-4803-82ae-dae529ae94fe/dqc_reference/reference_markers.fasta -out GCF_002811245.1_ASM281124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:49,436] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:49,446] [INFO] Selected 18 target genomes.
[2024-01-24 11:34:49,447] [INFO] Target genome list was writen to GCF_002811245.1_ASM281124v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:49,454] [INFO] Task started: fastANI
[2024-01-24 11:34:49,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg85017b12-fb6f-4847-af0c-434a6cdebceb/GCF_002811245.1_ASM281124v1_genomic.fna.gz --refList GCF_002811245.1_ASM281124v1_genomic.fna/target_genomes.txt --output GCF_002811245.1_ASM281124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:04,383] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:04,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6a197b2-85b6-4803-82ae-dae529ae94fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:04,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6a197b2-85b6-4803-82ae-dae529ae94fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:04,399] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:04,399] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:04,400] [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 salilacus	strain=DSG-S6	GCA_002811245.1	1323749	1323749	type	True	100.0	1157	1160	95	inconclusive
Vibrio pacinii	strain=DSM 19139	GCA_000711795.1	170674	170674	type	True	95.5386	1006	1160	95	inconclusive
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	80.9348	590	1160	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	80.9244	602	1160	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	80.9036	611	1160	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.7415	568	1160	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.5787	551	1160	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	80.1512	433	1160	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	80.0802	437	1160	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	79.7347	378	1160	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	79.7324	366	1160	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	79.7144	313	1160	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.4804	366	1160	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.3739	391	1160	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.3165	390	1160	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.9716	299	1160	95	below_threshold
Vibrio mimicus	strain=NCTC11435	GCA_900460385.1	674	674	type	True	78.4384	293	1160	95	below_threshold
Vibrio mimicus	strain=CAIM 602	GCA_000338875.1	674	674	type	True	78.3384	291	1160	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:04,401] [INFO] DFAST Taxonomy check result was written to GCF_002811245.1_ASM281124v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:04,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:04,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:04,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6a197b2-85b6-4803-82ae-dae529ae94fe/dqc_reference/checkm_data
[2024-01-24 11:35:04,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:04,442] [INFO] Task started: CheckM
[2024-01-24 11:35:04,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002811245.1_ASM281124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002811245.1_ASM281124v1_genomic.fna/checkm_input GCF_002811245.1_ASM281124v1_genomic.fna/checkm_result
[2024-01-24 11:35:35,734] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:35,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:35,751] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:35,752] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:35,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002811245.1_ASM281124v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:35,752] [INFO] Task started: Blastn
[2024-01-24 11:35:35,752] [INFO] Running command: blastn -query GCF_002811245.1_ASM281124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6a197b2-85b6-4803-82ae-dae529ae94fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_002811245.1_ASM281124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:36,922] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:36,925] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:36,925] [INFO] Target genome list was writen to GCF_002811245.1_ASM281124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:36,936] [INFO] Task started: fastANI
[2024-01-24 11:35:36,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg85017b12-fb6f-4847-af0c-434a6cdebceb/GCF_002811245.1_ASM281124v1_genomic.fna.gz --refList GCF_002811245.1_ASM281124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002811245.1_ASM281124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:50,652] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:50,665] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:50,665] [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_002811245.1	s__Vibrio salilacus	100.0	1157	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	conclusive
GCF_000711795.1	s__Vibrio pacinii	95.5386	1006	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	conclusive
GCF_013369335.1	s__Vibrio sp013369335	81.5535	679	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001695575.1	s__Vibrio europaeus	80.9285	601	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000189255.1	s__Vibrio brasiliensis	80.8892	554	1160	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	80.8406	576	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967545.1	s__Vibrio galatheae	80.6605	544	1160	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	80.635	518	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000775715.1	s__Vibrio tubiashii_A	80.5886	525	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970385.1	s__Vibrio aquaticus	80.5787	551	1160	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	80.5523	505	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_013114545.1	s__Vibrio sp013114545	80.5509	547	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806575.1	s__Vibrio hepatarius_A	80.0448	486	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_001274785.1	s__Vibrio hepatarius	80.0298	497	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_000222585.1	s__Vibrio scophthalmi	79.7281	378	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_000338875.1	s__Vibrio mimicus	78.3509	290	1160	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.81	0.94	0.91	26	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:50,667] [INFO] GTDB search result was written to GCF_002811245.1_ASM281124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:50,668] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:50,671] [INFO] DFAST_QC result json was written to GCF_002811245.1_ASM281124v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:50,672] [INFO] DFAST_QC completed!
[2024-01-24 11:35:50,672] [INFO] Total running time: 0h1m14s