[2024-01-24 12:00:36,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cc5b859-7a08-4862-b12c-9ab977cc1382/dqc_reference
[2024-01-24 12:00:39,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,378] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,378] [INFO] Running command: gunzip -c /var/lib/cwl/stgdee17fec-77fb-4320-91e1-004025abae00/GCF_030409635.1_ASM3040963v1_genomic.fna.gz | prodigal -d GCF_030409635.1_ASM3040963v1_genomic.fna/cds.fna -a GCF_030409635.1_ASM3040963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:51,417] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:51,418] [INFO] Task started: HMMsearch
[2024-01-24 12:00:51,418] [INFO] Running command: hmmsearch --tblout GCF_030409635.1_ASM3040963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cc5b859-7a08-4862-b12c-9ab977cc1382/dqc_reference/reference_markers.hmm GCF_030409635.1_ASM3040963v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:51,698] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:51,699] [INFO] Found 6/6 markers.
[2024-01-24 12:00:51,741] [INFO] Query marker FASTA was written to GCF_030409635.1_ASM3040963v1_genomic.fna/markers.fasta
[2024-01-24 12:00:51,742] [INFO] Task started: Blastn
[2024-01-24 12:00:51,742] [INFO] Running command: blastn -query GCF_030409635.1_ASM3040963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc5b859-7a08-4862-b12c-9ab977cc1382/dqc_reference/reference_markers.fasta -out GCF_030409635.1_ASM3040963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:52,566] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:52,571] [INFO] Selected 28 target genomes.
[2024-01-24 12:00:52,571] [INFO] Target genome list was writen to GCF_030409635.1_ASM3040963v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:52,582] [INFO] Task started: fastANI
[2024-01-24 12:00:52,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgdee17fec-77fb-4320-91e1-004025abae00/GCF_030409635.1_ASM3040963v1_genomic.fna.gz --refList GCF_030409635.1_ASM3040963v1_genomic.fna/target_genomes.txt --output GCF_030409635.1_ASM3040963v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:15,447] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:15,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cc5b859-7a08-4862-b12c-9ab977cc1382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:15,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cc5b859-7a08-4862-b12c-9ab977cc1382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:15,478] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:01:15,478] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:01:15,479] [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 orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	80.8928	344	1633	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	80.83	342	1633	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.7531	356	1633	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	80.7245	364	1633	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.6432	345	1633	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.5303	341	1633	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	80.49	343	1633	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.4386	331	1633	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	80.3786	268	1633	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	80.2914	330	1633	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.2892	319	1633	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.1848	356	1633	95	below_threshold
Vibrio variabilis	strain=CAIM 1454	GCA_003263785.1	990271	990271	type	True	80.0881	308	1633	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.0316	319	1633	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	79.9551	353	1633	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	79.9231	359	1633	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	79.8972	332	1633	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	79.815	290	1633	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	79.7903	288	1633	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	79.7667	331	1633	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	79.6933	342	1633	95	below_threshold
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	79.6634	274	1633	95	below_threshold
Vibrio mediterranei		GCA_900088415.1	689	689	type	True	79.6144	305	1633	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	79.5913	303	1633	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	79.5814	316	1633	95	below_threshold
Vibrio mediterranei	strain=NBRC 15635	GCA_001591125.1	689	689	type	True	79.5606	301	1633	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	79.5496	310	1633	95	below_threshold
Vibrio fluvialis	strain=NBRC 103150	GCA_001598835.1	676	676	type	True	79.1727	273	1633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:15,480] [INFO] DFAST Taxonomy check result was written to GCF_030409635.1_ASM3040963v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:15,482] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:15,482] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:15,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cc5b859-7a08-4862-b12c-9ab977cc1382/dqc_reference/checkm_data
[2024-01-24 12:01:15,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:15,532] [INFO] Task started: CheckM
[2024-01-24 12:01:15,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409635.1_ASM3040963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409635.1_ASM3040963v1_genomic.fna/checkm_input GCF_030409635.1_ASM3040963v1_genomic.fna/checkm_result
[2024-01-24 12:01:56,279] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:56,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:56,308] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:56,308] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:56,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409635.1_ASM3040963v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:56,309] [INFO] Task started: Blastn
[2024-01-24 12:01:56,309] [INFO] Running command: blastn -query GCF_030409635.1_ASM3040963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc5b859-7a08-4862-b12c-9ab977cc1382/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409635.1_ASM3040963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:57,468] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:57,473] [INFO] Selected 24 target genomes.
[2024-01-24 12:01:57,473] [INFO] Target genome list was writen to GCF_030409635.1_ASM3040963v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:57,500] [INFO] Task started: fastANI
[2024-01-24 12:01:57,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgdee17fec-77fb-4320-91e1-004025abae00/GCF_030409635.1_ASM3040963v1_genomic.fna.gz --refList GCF_030409635.1_ASM3040963v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409635.1_ASM3040963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:17,532] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:17,562] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:02:17,562] [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_010587385.1	s__Vibrio astriarenae	83.5959	914	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	96.60	0.82	0.82	2	-
GCF_002906655.1	s__Vibrio hyugaensis	80.8469	367	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_000772105.1	s__Vibrio tubiashii	80.7322	340	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_002163755.1	s__Vibrio campbellii	80.5577	352	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_001695575.1	s__Vibrio europaeus	80.4941	343	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_013114545.1	s__Vibrio sp013114545	80.4548	349	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954585.1	s__Vibrio chagasii_A	80.3447	325	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_001012815.1	s__Vibrio mexicanus	80.2239	344	1633	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	80.2186	356	1633	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	80.2123	328	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_009938165.1	s__Vibrio taketomensis	80.1855	333	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_003970385.1	s__Vibrio aquaticus	80.1692	357	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003263845.1	s__Vibrio aestivus	80.1174	332	1633	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	80.0572	339	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_000967545.1	s__Vibrio galatheae	80.0531	296	1633	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	80.043	315	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_001635455.1	s__Vibrio sp001635455	80.0297	303	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460245.1	s__Vibrio fluvialis	79.9883	292	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_000817815.1	s__Vibrio owensii	79.9443	359	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_013113835.1	s__Vibrio sp013113835	79.888	319	1633	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	79.8291	317	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_000967495.1	s__Vibrio neptunius	79.693	285	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
GCF_000222585.1	s__Vibrio scophthalmi	79.5334	311	1633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_000830505.1	s__Vibrio mytili	79.5183	273	1633	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 12:02:17,565] [INFO] GTDB search result was written to GCF_030409635.1_ASM3040963v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:17,565] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:17,571] [INFO] DFAST_QC result json was written to GCF_030409635.1_ASM3040963v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:17,571] [INFO] DFAST_QC completed!
[2024-01-24 12:02:17,571] [INFO] Total running time: 0h1m41s