[2024-01-25 17:46:20,437] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:20,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:20,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg96f4e1c2-c300-4d6e-bb63-9ec5d6b0bf9c/dqc_reference
[2024-01-25 17:46:21,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:21,613] [INFO] Task started: Prodigal
[2024-01-25 17:46:21,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg654dfc6b-8399-4770-a5ae-653f40d8a7e4/GCF_020166345.1_ASM2016634v1_genomic.fna.gz | prodigal -d GCF_020166345.1_ASM2016634v1_genomic.fna/cds.fna -a GCF_020166345.1_ASM2016634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:30,674] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:30,674] [INFO] Task started: HMMsearch
[2024-01-25 17:46:30,674] [INFO] Running command: hmmsearch --tblout GCF_020166345.1_ASM2016634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96f4e1c2-c300-4d6e-bb63-9ec5d6b0bf9c/dqc_reference/reference_markers.hmm GCF_020166345.1_ASM2016634v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:30,920] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:30,921] [INFO] Found 6/6 markers.
[2024-01-25 17:46:30,952] [INFO] Query marker FASTA was written to GCF_020166345.1_ASM2016634v1_genomic.fna/markers.fasta
[2024-01-25 17:46:30,952] [INFO] Task started: Blastn
[2024-01-25 17:46:30,952] [INFO] Running command: blastn -query GCF_020166345.1_ASM2016634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96f4e1c2-c300-4d6e-bb63-9ec5d6b0bf9c/dqc_reference/reference_markers.fasta -out GCF_020166345.1_ASM2016634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:31,595] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:31,597] [INFO] Selected 24 target genomes.
[2024-01-25 17:46:31,598] [INFO] Target genome list was writen to GCF_020166345.1_ASM2016634v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:31,621] [INFO] Task started: fastANI
[2024-01-25 17:46:31,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg654dfc6b-8399-4770-a5ae-653f40d8a7e4/GCF_020166345.1_ASM2016634v1_genomic.fna.gz --refList GCF_020166345.1_ASM2016634v1_genomic.fna/target_genomes.txt --output GCF_020166345.1_ASM2016634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:47,565] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:47,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96f4e1c2-c300-4d6e-bb63-9ec5d6b0bf9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:47,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96f4e1c2-c300-4d6e-bb63-9ec5d6b0bf9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:47,580] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:46:47,580] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:46:47,580] [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
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.7296	343	1076	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.5014	388	1076	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.1827	369	1076	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.1672	407	1076	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.1488	409	1076	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.0785	391	1076	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.05	333	1076	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	78.0422	356	1076	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.9655	322	1076	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	77.8985	249	1076	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.8888	257	1076	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	77.8761	268	1076	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.8737	247	1076	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.842	269	1076	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.6778	210	1076	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.6587	337	1076	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.5228	219	1076	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.433	102	1076	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.3727	203	1076	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.9974	123	1076	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.9536	123	1076	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.9221	161	1076	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.6823	103	1076	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.6798	170	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:47,582] [INFO] DFAST Taxonomy check result was written to GCF_020166345.1_ASM2016634v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:47,582] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:47,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:47,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96f4e1c2-c300-4d6e-bb63-9ec5d6b0bf9c/dqc_reference/checkm_data
[2024-01-25 17:46:47,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:47,619] [INFO] Task started: CheckM
[2024-01-25 17:46:47,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020166345.1_ASM2016634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020166345.1_ASM2016634v1_genomic.fna/checkm_input GCF_020166345.1_ASM2016634v1_genomic.fna/checkm_result
[2024-01-25 17:47:17,149] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:17,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:17,167] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:17,167] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:17,167] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020166345.1_ASM2016634v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:17,168] [INFO] Task started: Blastn
[2024-01-25 17:47:17,168] [INFO] Running command: blastn -query GCF_020166345.1_ASM2016634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96f4e1c2-c300-4d6e-bb63-9ec5d6b0bf9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_020166345.1_ASM2016634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:18,126] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:18,130] [INFO] Selected 20 target genomes.
[2024-01-25 17:47:18,130] [INFO] Target genome list was writen to GCF_020166345.1_ASM2016634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:18,153] [INFO] Task started: fastANI
[2024-01-25 17:47:18,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg654dfc6b-8399-4770-a5ae-653f40d8a7e4/GCF_020166345.1_ASM2016634v1_genomic.fna.gz --refList GCF_020166345.1_ASM2016634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020166345.1_ASM2016634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:32,149] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:32,161] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:47:32,161] [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_003335675.1	s__Winogradskyella sp003335675	93.4027	808	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709615.1	s__Winogradskyella ouciana	78.7421	342	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCF_005869935.1	s__Winogradskyella algicola	78.4958	389	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203985.1	s__Winogradskyella sp019203985	78.4389	332	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.3795	417	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971725.1	s__Winogradskyella sp001971725	78.2765	355	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	78.2615	341	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722255.1	s__Winogradskyella sp002722255	78.2197	331	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	78.1733	370	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	78.1579	408	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014243395.1	s__Winogradskyella flava	78.0791	391	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	78.0301	329	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	78.0285	268	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCF_900099995.1	s__Winogradskyella thalassocola	77.9655	322	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217215.1	s__Winogradskyella epiphytica	77.9184	253	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003386165.1	s__Winogradskyella eximia	77.8865	345	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346845.1	s__Winogradskyella wandonensis	77.8737	247	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	77.8706	347	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.5228	219	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	77.4512	178	1076	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:32,163] [INFO] GTDB search result was written to GCF_020166345.1_ASM2016634v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:32,163] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:32,167] [INFO] DFAST_QC result json was written to GCF_020166345.1_ASM2016634v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:32,167] [INFO] DFAST_QC completed!
[2024-01-25 17:47:32,167] [INFO] Total running time: 0h1m12s