[2024-01-24 14:19:59,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d2cfbcb-d5e6-4d9b-a09f-c66aafa50ef8/dqc_reference
[2024-01-24 14:20:01,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,345] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,346] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9e01f52-3b03-421a-b403-413679ec76d1/GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna.gz | prodigal -d GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/cds.fna -a GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:12,551] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:12,552] [INFO] Task started: HMMsearch
[2024-01-24 14:20:12,552] [INFO] Running command: hmmsearch --tblout GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d2cfbcb-d5e6-4d9b-a09f-c66aafa50ef8/dqc_reference/reference_markers.hmm GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:12,961] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:12,962] [INFO] Found 6/6 markers.
[2024-01-24 14:20:13,005] [INFO] Query marker FASTA was written to GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/markers.fasta
[2024-01-24 14:20:13,005] [INFO] Task started: Blastn
[2024-01-24 14:20:13,005] [INFO] Running command: blastn -query GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d2cfbcb-d5e6-4d9b-a09f-c66aafa50ef8/dqc_reference/reference_markers.fasta -out GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:13,836] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:13,840] [INFO] Selected 29 target genomes.
[2024-01-24 14:20:13,841] [INFO] Target genome list was writen to GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/target_genomes.txt
[2024-01-24 14:20:13,883] [INFO] Task started: fastANI
[2024-01-24 14:20:13,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9e01f52-3b03-421a-b403-413679ec76d1/GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna.gz --refList GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/target_genomes.txt --output GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:36,260] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:36,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d2cfbcb-d5e6-4d9b-a09f-c66aafa50ef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:36,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d2cfbcb-d5e6-4d9b-a09f-c66aafa50ef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:36,287] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:36,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:36,288] [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 marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	100.0	1589	1590	95	conclusive
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.382	223	1590	95	below_threshold
Vibrio natriegens	strain=CCUG 16371	GCA_001680045.1	691	691	type	True	80.2088	232	1590	95	below_threshold
Vibrio vulnificus	strain=NCTC13647	GCA_900460565.1	672	672	type	True	80.1417	230	1590	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.0909	226	1590	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	80.0722	238	1590	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_002224265.1	672	672	type	True	80.0557	227	1590	95	below_threshold
Vibrio cidicii	strain=2756-81	GCA_009763805.1	1763883	1763883	type	True	79.9162	198	1590	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	79.8996	263	1590	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	79.896	257	1590	95	below_threshold
Vibrio navarrensis	strain=ATCC 51183	GCA_000764325.1	29495	29495	type	True	79.8503	184	1590	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.8467	241	1590	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.8106	221	1590	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	79.7826	225	1590	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.6427	244	1590	95	below_threshold
Vibrio aestuarianus subsp. francensis	strain=02/041	GCA_012395215.1	1443279	28171	type	True	79.6279	245	1590	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	79.3101	236	1590	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.2311	244	1590	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	79.1964	246	1590	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.1772	181	1590	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	79.1708	217	1590	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	79.1641	221	1590	95	below_threshold
Vibrio sinensis	strain=BEI233	GCA_003605645.1	2302434	2302434	type	True	79.159	212	1590	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	79.148	237	1590	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	79.1033	247	1590	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	79.0998	237	1590	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	79.0584	233	1590	95	below_threshold
Vibrio vulnificus	strain=NBRC 15645	GCA_001591065.1	672	672	type	True	79.049	214	1590	95	below_threshold
Vibrio aestuarianus	strain=LMG 7909	GCA_012395185.1	28171	28171	type	True	78.941	243	1590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:36,290] [INFO] DFAST Taxonomy check result was written to GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/tc_result.tsv
[2024-01-24 14:20:36,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:36,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:36,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d2cfbcb-d5e6-4d9b-a09f-c66aafa50ef8/dqc_reference/checkm_data
[2024-01-24 14:20:36,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:36,347] [INFO] Task started: CheckM
[2024-01-24 14:20:36,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/checkm_input GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/checkm_result
[2024-01-24 14:21:15,247] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:15,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:15,289] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:15,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:15,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/markers.fasta)
[2024-01-24 14:21:15,290] [INFO] Task started: Blastn
[2024-01-24 14:21:15,290] [INFO] Running command: blastn -query GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d2cfbcb-d5e6-4d9b-a09f-c66aafa50ef8/dqc_reference/reference_markers_gtdb.fasta -out GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:16,462] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:16,465] [INFO] Selected 26 target genomes.
[2024-01-24 14:21:16,466] [INFO] Target genome list was writen to GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:16,502] [INFO] Task started: fastANI
[2024-01-24 14:21:16,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9e01f52-3b03-421a-b403-413679ec76d1/GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna.gz --refList GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/target_genomes_gtdb.txt --output GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:37,307] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:37,338] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:37,338] [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_003263805.1	s__Vibrio marisflavi	99.8017	1452	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002224265.1	s__Vibrio vulnificus	80.0949	230	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.11	95.22	0.91	0.85	225	-
GCF_000176235.1	s__Vibrio orientalis	79.8857	260	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001695575.1	s__Vibrio europaeus	79.833	251	1590	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	79.8021	222	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_000695685.1	s__Vibrio fortis	79.572	210	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_004551525.1	s__Vibrio ouci	79.5219	240	1590	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	79.3923	226	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001048675.1	s__Vibrio diabolicus	79.3711	236	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_013369385.1	s__Vibrio sp013369385	79.3561	201	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775715.1	s__Vibrio tubiashii_A	79.3388	229	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350325.1	s__Vibrio rhodolitus	79.3229	236	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_015278125.1	s__Vibrio sp015278125	79.2613	215	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827885.1	s__Vibrio renipiscarius	79.2355	220	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000257205.1	s__Vibrio ordalii	79.219	175	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.90	98.90	0.96	0.96	2	-
GCF_003970385.1	s__Vibrio aquaticus	79.2147	244	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001989995.2	s__Vibrio anguillarum	79.2081	191	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.39	98.01	0.89	0.80	121	-
GCA_003263845.1	s__Vibrio aestivus	79.1786	229	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605645.1	s__Vibrio sinensis	79.171	212	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591105.1	s__Vibrio nereis	79.1576	236	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000222605.1	s__Vibrio ichthyoenteri	79.1483	216	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089835.1	s__Vibrio thalassae	79.126	202	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCF_000808535.1	s__Vibrio sinaloensis	79.0912	251	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCA_018223135.1	s__Vibrio sp018223135	79.0541	209	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395185.1	s__Vibrio aestuarianus	78.9656	241	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.70	96.75	0.86	0.80	14	-
GCA_018222805.1	s__Vibrio sp018222805	78.5874	180	1590	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 14:21:37,340] [INFO] GTDB search result was written to GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:37,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:37,350] [INFO] DFAST_QC result json was written to GCF_921294215.1_V_marisflavi_CECT7928_genomic.fna/dqc_result.json
[2024-01-24 14:21:37,350] [INFO] DFAST_QC completed!
[2024-01-24 14:21:37,350] [INFO] Total running time: 0h1m37s