[2024-01-24 14:30:30,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg86666e5e-a3f0-48df-a194-19afc4eedc41/dqc_reference
[2024-01-24 14:30:33,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,669] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,670] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b4398b1-6756-42b4-9cb8-4e6b8f17aaec/GCF_002257545.1_ASM225754v1_genomic.fna.gz | prodigal -d GCF_002257545.1_ASM225754v1_genomic.fna/cds.fna -a GCF_002257545.1_ASM225754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:44,239] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:44,239] [INFO] Task started: HMMsearch
[2024-01-24 14:30:44,239] [INFO] Running command: hmmsearch --tblout GCF_002257545.1_ASM225754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86666e5e-a3f0-48df-a194-19afc4eedc41/dqc_reference/reference_markers.hmm GCF_002257545.1_ASM225754v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:44,546] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:44,547] [INFO] Found 6/6 markers.
[2024-01-24 14:30:44,580] [INFO] Query marker FASTA was written to GCF_002257545.1_ASM225754v1_genomic.fna/markers.fasta
[2024-01-24 14:30:44,580] [INFO] Task started: Blastn
[2024-01-24 14:30:44,581] [INFO] Running command: blastn -query GCF_002257545.1_ASM225754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86666e5e-a3f0-48df-a194-19afc4eedc41/dqc_reference/reference_markers.fasta -out GCF_002257545.1_ASM225754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:45,421] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:45,426] [INFO] Selected 16 target genomes.
[2024-01-24 14:30:45,426] [INFO] Target genome list was writen to GCF_002257545.1_ASM225754v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:45,469] [INFO] Task started: fastANI
[2024-01-24 14:30:45,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b4398b1-6756-42b4-9cb8-4e6b8f17aaec/GCF_002257545.1_ASM225754v1_genomic.fna.gz --refList GCF_002257545.1_ASM225754v1_genomic.fna/target_genomes.txt --output GCF_002257545.1_ASM225754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:03,287] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:03,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86666e5e-a3f0-48df-a194-19afc4eedc41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:03,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86666e5e-a3f0-48df-a194-19afc4eedc41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:03,301] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:31:03,301] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:31:03,302] [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 qinghaiensis	strain=Q67	GCA_002257545.1	2025808	2025808	type	True	100.0	1335	1338	95	inconclusive
Vibrio anguillarum	strain=DSM 21597	GCA_001989995.2	55601	55601	type	True	96.1658	1034	1338	95	inconclusive
Vibrio anguillarum	strain=NCTC12159	GCA_900452855.1	55601	55601	type	True	96.0948	1090	1338	95	inconclusive
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	81.8256	679	1338	95	below_threshold
Vibrio aestuarianus subsp. francensis	strain=02/041	GCA_012395215.1	1443279	28171	type	True	81.798	689	1338	95	below_threshold
Vibrio aestuarianus	strain=LMG 7909	GCA_012395185.1	28171	28171	type	True	81.6492	696	1338	95	below_threshold
Vibrio cidicii	strain=2756-81	GCA_009763805.1	1763883	1763883	type	True	80.0377	380	1338	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	79.9522	215	1338	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	79.6347	432	1338	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	79.5174	360	1338	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.5161	317	1338	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.4945	312	1338	95	below_threshold
Vibrio navarrensis	strain=ATCC 51183	GCA_000764325.1	29495	29495	type	True	79.4208	369	1338	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.12	349	1338	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	79.115	290	1338	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	78.8063	320	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:03,303] [INFO] DFAST Taxonomy check result was written to GCF_002257545.1_ASM225754v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:03,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:03,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:03,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86666e5e-a3f0-48df-a194-19afc4eedc41/dqc_reference/checkm_data
[2024-01-24 14:31:03,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:03,351] [INFO] Task started: CheckM
[2024-01-24 14:31:03,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002257545.1_ASM225754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002257545.1_ASM225754v1_genomic.fna/checkm_input GCF_002257545.1_ASM225754v1_genomic.fna/checkm_result
[2024-01-24 14:31:42,094] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:42,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:42,115] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:42,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:42,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002257545.1_ASM225754v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:42,116] [INFO] Task started: Blastn
[2024-01-24 14:31:42,117] [INFO] Running command: blastn -query GCF_002257545.1_ASM225754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86666e5e-a3f0-48df-a194-19afc4eedc41/dqc_reference/reference_markers_gtdb.fasta -out GCF_002257545.1_ASM225754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:43,364] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:43,367] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:43,368] [INFO] Target genome list was writen to GCF_002257545.1_ASM225754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:43,387] [INFO] Task started: fastANI
[2024-01-24 14:31:43,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b4398b1-6756-42b4-9cb8-4e6b8f17aaec/GCF_002257545.1_ASM225754v1_genomic.fna.gz --refList GCF_002257545.1_ASM225754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002257545.1_ASM225754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:02,919] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:02,934] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:02,935] [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
GCA_000257205.1	s__Vibrio ordalii	98.8214	970	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.90	98.90	0.96	0.96	2	conclusive
GCF_001989995.2	s__Vibrio anguillarum	96.1658	1034	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.39	98.01	0.89	0.80	121	-
GCF_012395185.1	s__Vibrio aestuarianus	81.6472	697	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.70	96.75	0.86	0.80	14	-
GCA_015767675.1	s__Vibrio sp000960595	80.2607	372	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.38	0.94	0.90	8	-
GCF_009763805.1	s__Vibrio cidicii	80.0685	377	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.20	97.77	0.90	0.87	8	-
GCF_000354175.2	s__Vibrio alginolyticus	79.9149	336	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_011064285.1	s__Vibrio ziniensis	79.6197	359	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363415.1	s__Vibrio aquimaris	79.5394	229	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019226825.1	s__Vibrio sp004804295	79.5054	356	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_000764325.1	s__Vibrio navarrensis	79.4084	371	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_013041605.1	s__Vibrio plantisponsor	79.1415	365	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_000222605.1	s__Vibrio ichthyoenteri	79.0901	291	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740015.1	s__Vibrio diazotrophicus	78.9244	369	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_014596725.1	s__Vibrio sp014596725	78.8758	359	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_003350325.1	s__Vibrio rhodolitus	78.8722	325	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_003350295.1	s__Vibrio tetraodonis	78.8612	217	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.28	95.28	0.88	0.88	2	-
GCF_000827885.1	s__Vibrio renipiscarius	78.8557	316	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004551525.1	s__Vibrio ouci	78.8543	333	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:02,936] [INFO] GTDB search result was written to GCF_002257545.1_ASM225754v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:02,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:02,942] [INFO] DFAST_QC result json was written to GCF_002257545.1_ASM225754v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:02,942] [INFO] DFAST_QC completed!
[2024-01-24 14:32:02,942] [INFO] Total running time: 0h1m33s