[2023-03-18 22:16:20,349] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:16:20,350] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:16:20,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e20e66b-211a-4c14-b67a-03dedb033643/dqc_reference
[2023-03-18 22:16:21,499] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:16:21,499] [INFO] Task started: Prodigal
[2023-03-18 22:16:21,499] [INFO] Running command: cat /var/lib/cwl/stg1ac5e5c3-b8ec-45af-b7d3-790d84ad41c4/OceanDNA-b6207.fa | prodigal -d OceanDNA-b6207/cds.fna -a OceanDNA-b6207/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:16:47,116] [INFO] Task succeeded: Prodigal
[2023-03-18 22:16:47,117] [INFO] Task started: HMMsearch
[2023-03-18 22:16:47,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b6207/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e20e66b-211a-4c14-b67a-03dedb033643/dqc_reference/reference_markers.hmm OceanDNA-b6207/protein.faa > /dev/null
[2023-03-18 22:16:47,348] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:16:47,348] [INFO] Found 6/6 markers.
[2023-03-18 22:16:47,376] [INFO] Query marker FASTA was written to OceanDNA-b6207/markers.fasta
[2023-03-18 22:16:47,376] [INFO] Task started: Blastn
[2023-03-18 22:16:47,376] [INFO] Running command: blastn -query OceanDNA-b6207/markers.fasta -db /var/lib/cwl/stg8e20e66b-211a-4c14-b67a-03dedb033643/dqc_reference/reference_markers.fasta -out OceanDNA-b6207/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:16:47,951] [INFO] Task succeeded: Blastn
[2023-03-18 22:16:47,952] [INFO] Selected 30 target genomes.
[2023-03-18 22:16:47,952] [INFO] Target genome list was writen to OceanDNA-b6207/target_genomes.txt
[2023-03-18 22:16:47,964] [INFO] Task started: fastANI
[2023-03-18 22:16:47,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac5e5c3-b8ec-45af-b7d3-790d84ad41c4/OceanDNA-b6207.fa --refList OceanDNA-b6207/target_genomes.txt --output OceanDNA-b6207/fastani_result.tsv --threads 1
[2023-03-18 22:17:04,943] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:04,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e20e66b-211a-4c14-b67a-03dedb033643/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:17:04,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e20e66b-211a-4c14-b67a-03dedb033643/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:17:04,956] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:17:04,956] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:17:04,956] [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
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.3782	88	1262	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	75.9016	81	1262	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	75.8071	60	1262	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	75.7905	60	1262	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	75.7715	54	1262	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	75.7674	57	1262	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	75.7485	64	1262	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.7204	66	1262	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	75.6937	62	1262	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	75.6876	61	1262	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	75.6836	59	1262	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	75.6823	66	1262	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	75.6772	69	1262	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	75.6753	58	1262	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	75.6747	69	1262	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	75.6535	60	1262	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	75.5581	58	1262	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	75.5303	63	1262	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	75.4488	53	1262	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	75.4324	52	1262	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	75.2508	62	1262	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:17:04,956] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6207/tc_result.tsv
[2023-03-18 22:17:04,957] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:17:04,957] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:17:04,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e20e66b-211a-4c14-b67a-03dedb033643/dqc_reference/checkm_data
[2023-03-18 22:17:04,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:17:04,964] [INFO] Task started: CheckM
[2023-03-18 22:17:04,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6207/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6207/checkm_input OceanDNA-b6207/checkm_result
[2023-03-18 22:18:08,330] [INFO] Task succeeded: CheckM
[2023-03-18 22:18:08,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:18:08,333] [INFO] ===== Completeness check finished =====
[2023-03-18 22:18:08,334] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:18:08,334] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6207/markers.fasta)
[2023-03-18 22:18:08,335] [INFO] Task started: Blastn
[2023-03-18 22:18:08,335] [INFO] Running command: blastn -query OceanDNA-b6207/markers.fasta -db /var/lib/cwl/stg8e20e66b-211a-4c14-b67a-03dedb033643/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6207/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:18:09,182] [INFO] Task succeeded: Blastn
[2023-03-18 22:18:09,183] [INFO] Selected 30 target genomes.
[2023-03-18 22:18:09,183] [INFO] Target genome list was writen to OceanDNA-b6207/target_genomes_gtdb.txt
[2023-03-18 22:18:09,211] [INFO] Task started: fastANI
[2023-03-18 22:18:09,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac5e5c3-b8ec-45af-b7d3-790d84ad41c4/OceanDNA-b6207.fa --refList OceanDNA-b6207/target_genomes_gtdb.txt --output OceanDNA-b6207/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:18:26,832] [INFO] Task succeeded: fastANI
[2023-03-18 22:18:26,846] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:18:26,846] [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_009901575.1	s__Leptobacterium sp009901575	76.1161	108	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260115.1	s__Joostella marina	75.9016	81	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	75.8071	60	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_014764305.1	s__Mesoflavibacter profundi	75.7905	60	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_004364175.1	s__Maribacter caenipelagi	75.7715	54	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	75.7674	57	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	75.7485	64	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	75.7023	53	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197735.1	s__Formosa sediminum	75.6937	62	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	75.6909	56	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	75.6845	57	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_900116665.1	s__Pustulibacterium marinum	75.6823	66	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154725.1	s__Kordia algicida	75.6772	69	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	75.6753	58	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746415.1	s__Saonia sp002746415	75.6706	54	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	75.6578	70	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_004366715.1	s__Meridianimaribacter flavus	75.6291	59	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_016734785.1	s__Galbibacter_A mesophilus	75.5232	72	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	75.4932	65	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646655.1	s__Yeosuana aromativorans	75.4488	53	1262	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:18:26,847] [INFO] GTDB search result was written to OceanDNA-b6207/result_gtdb.tsv
[2023-03-18 22:18:26,847] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:18:26,850] [INFO] DFAST_QC result json was written to OceanDNA-b6207/dqc_result.json
[2023-03-18 22:18:26,850] [INFO] DFAST_QC completed!
[2023-03-18 22:18:26,851] [INFO] Total running time: 0h2m7s