[2024-01-25 18:37:05,493] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:05,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:05,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg5be7b277-99b0-4c0b-9930-21be724ae034/dqc_reference
[2024-01-25 18:37:06,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:06,699] [INFO] Task started: Prodigal
[2024-01-25 18:37:06,700] [INFO] Running command: gunzip -c /var/lib/cwl/stg05cdd840-2e0e-4413-a0e3-64fe2817f3d0/GCF_026191655.1_ASM2619165v1_genomic.fna.gz | prodigal -d GCF_026191655.1_ASM2619165v1_genomic.fna/cds.fna -a GCF_026191655.1_ASM2619165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:15,980] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:15,981] [INFO] Task started: HMMsearch
[2024-01-25 18:37:15,981] [INFO] Running command: hmmsearch --tblout GCF_026191655.1_ASM2619165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5be7b277-99b0-4c0b-9930-21be724ae034/dqc_reference/reference_markers.hmm GCF_026191655.1_ASM2619165v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:16,241] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:16,242] [INFO] Found 6/6 markers.
[2024-01-25 18:37:16,282] [INFO] Query marker FASTA was written to GCF_026191655.1_ASM2619165v1_genomic.fna/markers.fasta
[2024-01-25 18:37:16,282] [INFO] Task started: Blastn
[2024-01-25 18:37:16,282] [INFO] Running command: blastn -query GCF_026191655.1_ASM2619165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5be7b277-99b0-4c0b-9930-21be724ae034/dqc_reference/reference_markers.fasta -out GCF_026191655.1_ASM2619165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:16,991] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:16,994] [INFO] Selected 34 target genomes.
[2024-01-25 18:37:16,994] [INFO] Target genome list was writen to GCF_026191655.1_ASM2619165v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:17,064] [INFO] Task started: fastANI
[2024-01-25 18:37:17,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg05cdd840-2e0e-4413-a0e3-64fe2817f3d0/GCF_026191655.1_ASM2619165v1_genomic.fna.gz --refList GCF_026191655.1_ASM2619165v1_genomic.fna/target_genomes.txt --output GCF_026191655.1_ASM2619165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:37:46,197] [INFO] Task succeeded: fastANI
[2024-01-25 18:37:46,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5be7b277-99b0-4c0b-9930-21be724ae034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:37:46,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5be7b277-99b0-4c0b-9930-21be724ae034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:37:46,216] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:37:46,216] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:37:46,217] [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 europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	81.1073	495	1485	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	80.9265	483	1485	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	80.8536	503	1485	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.8326	398	1485	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	80.7926	414	1485	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	80.6713	457	1485	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.6517	457	1485	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	80.6267	464	1485	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.5687	473	1485	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	80.5631	463	1485	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	80.4716	423	1485	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	80.4444	427	1485	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.4108	443	1485	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	80.3874	416	1485	95	below_threshold
Vibrio maerlii	strain=G62	GCA_003415655.1	2231648	2231648	type	True	80.2799	370	1485	95	below_threshold
Vibrio profundi	strain=TP187	GCA_005281835.1	1774960	1774960	type	True	80.2725	449	1485	95	below_threshold
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	80.2154	276	1485	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.0887	377	1485	95	below_threshold
Vibrio thalassae	strain=CECT8203	GCA_900089835.1	1243014	1243014	type	True	80.0632	318	1485	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	80.0393	391	1485	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	79.9151	429	1485	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.915	347	1485	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	79.9115	381	1485	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.8439	354	1485	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	79.6909	347	1485	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	79.6562	379	1485	95	below_threshold
Vibrio ishigakensis	strain=JCM 19231	GCA_024347675.1	1481914	1481914	type	True	79.6518	215	1485	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	79.6238	362	1485	95	below_threshold
Vibrio aquimaris	strain=THAF100	GCA_009363415.1	2587862	2587862	type	True	79.44	234	1485	95	below_threshold
Vibrio gallicus	strain=CIP 107863	GCA_024346875.1	190897	190897	type	True	79.2555	172	1485	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	79.0513	239	1485	95	below_threshold
Vibrio palustris	strain=CECT 9027	GCA_024346995.1	1918946	1918946	type	True	78.734	159	1485	95	below_threshold
Vibrio metschnikovii	strain=CIP 69.14	GCA_000176155.1	28172	28172	type	True	78.6218	211	1485	95	below_threshold
Vibrio palustris	strain=CECT 9027	GCA_900162645.1	1918946	1918946	type	True	78.6164	161	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:37:46,218] [INFO] DFAST Taxonomy check result was written to GCF_026191655.1_ASM2619165v1_genomic.fna/tc_result.tsv
[2024-01-25 18:37:46,218] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:37:46,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:37:46,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5be7b277-99b0-4c0b-9930-21be724ae034/dqc_reference/checkm_data
[2024-01-25 18:37:46,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:37:46,268] [INFO] Task started: CheckM
[2024-01-25 18:37:46,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026191655.1_ASM2619165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026191655.1_ASM2619165v1_genomic.fna/checkm_input GCF_026191655.1_ASM2619165v1_genomic.fna/checkm_result
[2024-01-25 18:38:17,729] [INFO] Task succeeded: CheckM
[2024-01-25 18:38:17,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:38:17,749] [INFO] ===== Completeness check finished =====
[2024-01-25 18:38:17,750] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:38:17,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026191655.1_ASM2619165v1_genomic.fna/markers.fasta)
[2024-01-25 18:38:17,752] [INFO] Task started: Blastn
[2024-01-25 18:38:17,752] [INFO] Running command: blastn -query GCF_026191655.1_ASM2619165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5be7b277-99b0-4c0b-9930-21be724ae034/dqc_reference/reference_markers_gtdb.fasta -out GCF_026191655.1_ASM2619165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:38:18,683] [INFO] Task succeeded: Blastn
[2024-01-25 18:38:18,688] [INFO] Selected 35 target genomes.
[2024-01-25 18:38:18,689] [INFO] Target genome list was writen to GCF_026191655.1_ASM2619165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:38:18,710] [INFO] Task started: fastANI
[2024-01-25 18:38:18,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg05cdd840-2e0e-4413-a0e3-64fe2817f3d0/GCF_026191655.1_ASM2619165v1_genomic.fna.gz --refList GCF_026191655.1_ASM2619165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026191655.1_ASM2619165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:38:51,892] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:51,915] [INFO] Found 35 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:38:51,916] [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_001695575.1	s__Vibrio europaeus	81.1205	494	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_004551525.1	s__Vibrio ouci	80.9877	493	1485	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	80.943	452	1485	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	80.8061	444	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189275.1	s__Vibrio sinaloensis_B	80.7955	444	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741985.1	s__Vibrio rotiferianus	80.795	413	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000189255.1	s__Vibrio brasiliensis	80.7795	453	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000817815.1	s__Vibrio owensii	80.6837	455	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_000775715.1	s__Vibrio tubiashii_A	80.6564	419	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399455.2	s__Vibrio bivalvicida	80.6397	463	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_002163755.1	s__Vibrio campbellii	80.6077	426	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000176235.1	s__Vibrio orientalis	80.5764	462	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003970385.1	s__Vibrio aquaticus	80.5561	474	1485	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	80.5232	402	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695685.1	s__Vibrio fortis	80.4891	419	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_005281815.1	s__Vibrio chagasii	80.4478	428	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCF_001591145.1	s__Vibrio harveyi	80.4339	444	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_013113835.1	s__Vibrio sp013113835	80.3423	450	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003415655.1	s__Vibrio maerlii	80.3101	368	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281835.1	s__Vibrio profundi	80.2935	447	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107935.1	s__Vibrio hangzhouensis	80.25	276	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635455.1	s__Vibrio sp001635455	80.2468	431	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000354175.2	s__Vibrio alginolyticus	80.2448	408	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_010587385.1	s__Vibrio astriarenae	80.1568	297	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	96.60	0.82	0.82	2	-
GCF_013369335.1	s__Vibrio sp013369335	80.1286	394	1485	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	80.0807	317	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCA_000755425.1	s__Vibrio maritimus_A	80.0579	313	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278125.1	s__Vibrio sp015278125	79.8981	373	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003263775.1	s__Vibrio maritimus	79.8862	332	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000287055.2	s__Vibrio sp000287055	79.6575	375	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.47	99.16	0.95	0.92	3	-
GCF_000222585.1	s__Vibrio scophthalmi	79.6238	362	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_009938165.1	s__Vibrio taketomensis	79.466	381	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_009363415.1	s__Vibrio aquimaris	79.4608	233	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933855.1	s__Vibrio penaeicida_A	79.4169	260	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162645.1	s__Vibrio palustris	78.6164	161	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:38:51,923] [INFO] GTDB search result was written to GCF_026191655.1_ASM2619165v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:38:51,925] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:38:51,931] [INFO] DFAST_QC result json was written to GCF_026191655.1_ASM2619165v1_genomic.fna/dqc_result.json
[2024-01-25 18:38:51,931] [INFO] DFAST_QC completed!
[2024-01-25 18:38:51,931] [INFO] Total running time: 0h1m46s