[2023-03-16 06:24:06,019] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:24:06,020] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:24:06,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg1257c751-005a-40c1-b1f7-76dd34252a20/dqc_reference
[2023-03-16 06:24:07,120] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:24:07,120] [INFO] Task started: Prodigal
[2023-03-16 06:24:07,120] [INFO] Running command: cat /var/lib/cwl/stg71f8ac4d-c071-4c04-8847-815c5bc7de62/OceanDNA-b9716.fa | prodigal -d OceanDNA-b9716/cds.fna -a OceanDNA-b9716/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:24:26,529] [INFO] Task succeeded: Prodigal
[2023-03-16 06:24:26,529] [INFO] Task started: HMMsearch
[2023-03-16 06:24:26,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b9716/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1257c751-005a-40c1-b1f7-76dd34252a20/dqc_reference/reference_markers.hmm OceanDNA-b9716/protein.faa > /dev/null
[2023-03-16 06:24:26,739] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:24:26,740] [INFO] Found 6/6 markers.
[2023-03-16 06:24:26,758] [INFO] Query marker FASTA was written to OceanDNA-b9716/markers.fasta
[2023-03-16 06:24:26,759] [INFO] Task started: Blastn
[2023-03-16 06:24:26,759] [INFO] Running command: blastn -query OceanDNA-b9716/markers.fasta -db /var/lib/cwl/stg1257c751-005a-40c1-b1f7-76dd34252a20/dqc_reference/reference_markers.fasta -out OceanDNA-b9716/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:24:27,397] [INFO] Task succeeded: Blastn
[2023-03-16 06:24:27,398] [INFO] Selected 30 target genomes.
[2023-03-16 06:24:27,398] [INFO] Target genome list was writen to OceanDNA-b9716/target_genomes.txt
[2023-03-16 06:24:27,415] [INFO] Task started: fastANI
[2023-03-16 06:24:27,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f8ac4d-c071-4c04-8847-815c5bc7de62/OceanDNA-b9716.fa --refList OceanDNA-b9716/target_genomes.txt --output OceanDNA-b9716/fastani_result.tsv --threads 1
[2023-03-16 06:24:45,243] [INFO] Task succeeded: fastANI
[2023-03-16 06:24:45,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1257c751-005a-40c1-b1f7-76dd34252a20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:24:45,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1257c751-005a-40c1-b1f7-76dd34252a20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:24:45,259] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:24:45,259] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:24:45,259] [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
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.6885	229	1015	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.6425	202	1015	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.6374	169	1015	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	77.6374	169	1015	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.6101	169	1015	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.5936	185	1015	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.5668	218	1015	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	77.5013	150	1015	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.4673	200	1015	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.4673	200	1015	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4419	179	1015	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	77.4107	228	1015	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.4041	156	1015	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	77.3918	211	1015	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.3782	209	1015	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.3553	201	1015	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.2734	217	1015	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.2601	197	1015	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.2549	203	1015	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	77.2461	211	1015	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.2005	223	1015	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.0181	118	1015	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.8414	196	1015	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.8328	141	1015	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.7578	122	1015	95	below_threshold
Aegicerativicinus sediminis	strain=SM2-F	GCA_015476115.1	2893202	2893202	type	True	76.7415	88	1015	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	76.5795	99	1015	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.5727	138	1015	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.498	123	1015	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.3799	141	1015	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:24:45,259] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9716/tc_result.tsv
[2023-03-16 06:24:45,259] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:24:45,259] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:24:45,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1257c751-005a-40c1-b1f7-76dd34252a20/dqc_reference/checkm_data
[2023-03-16 06:24:45,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:24:45,265] [INFO] Task started: CheckM
[2023-03-16 06:24:45,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9716/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9716/checkm_input OceanDNA-b9716/checkm_result
[2023-03-16 06:25:34,922] [INFO] Task succeeded: CheckM
[2023-03-16 06:25:34,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:25:34,925] [INFO] ===== Completeness check finished =====
[2023-03-16 06:25:34,925] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:25:34,925] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9716/markers.fasta)
[2023-03-16 06:25:34,926] [INFO] Task started: Blastn
[2023-03-16 06:25:34,926] [INFO] Running command: blastn -query OceanDNA-b9716/markers.fasta -db /var/lib/cwl/stg1257c751-005a-40c1-b1f7-76dd34252a20/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9716/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:25:35,826] [INFO] Task succeeded: Blastn
[2023-03-16 06:25:35,827] [INFO] Selected 25 target genomes.
[2023-03-16 06:25:35,827] [INFO] Target genome list was writen to OceanDNA-b9716/target_genomes_gtdb.txt
[2023-03-16 06:25:35,879] [INFO] Task started: fastANI
[2023-03-16 06:25:35,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg71f8ac4d-c071-4c04-8847-815c5bc7de62/OceanDNA-b9716.fa --refList OceanDNA-b9716/target_genomes_gtdb.txt --output OceanDNA-b9716/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:25:50,850] [INFO] Task succeeded: fastANI
[2023-03-16 06:25:50,863] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:25:50,864] [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_001874335.1	s__MedPE-SWsnd-G2 sp001874335	99.9932	994	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MedPE-SWsnd-G2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002162765.1	s__MAAR01 sp002162765	77.7908	198	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.7663	257	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425645.1	s__Gaetbulibacter saemankumensis	77.7068	162	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.692	228	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.6888	246	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_009741275.1	s__Winogradskyella endarachnes	77.6415	200	1015	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	77.6332	205	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.6043	237	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337215.1	s__Oceanihabitans sediminis	77.5816	187	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001747085.1	s__Algibacter_C aquaticus	77.5349	195	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	77.4724	186	1015	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	77.4562	200	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007827365.1	s__Olleya sp002323495	77.439	200	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_900129745.1	s__Winogradskyella jejuensis	77.4074	155	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013285155.1	s__Winogradskyella undariae	77.4055	227	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_013403925.1	s__Winogradskyella wichelsiae	77.3861	210	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	77.3847	181	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645385.1	s__Winogradskyella sp015645385	77.3633	200	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	77.337	213	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	77.2651	237	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	77.2533	196	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	77.0561	152	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.8413	193	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827605.1	s__Jejuia sp016827605	76.8328	141	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:25:50,864] [INFO] GTDB search result was written to OceanDNA-b9716/result_gtdb.tsv
[2023-03-16 06:25:50,864] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:25:50,867] [INFO] DFAST_QC result json was written to OceanDNA-b9716/dqc_result.json
[2023-03-16 06:25:50,867] [INFO] DFAST_QC completed!
[2023-03-16 06:25:50,867] [INFO] Total running time: 0h1m45s