[2023-03-17 22:54:24,150] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:54:24,150] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:54:24,150] [INFO] DQC Reference Directory: /var/lib/cwl/stgca7d0b72-6c9c-4a30-9954-7eb112482110/dqc_reference
[2023-03-17 22:54:25,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:54:25,239] [INFO] Task started: Prodigal
[2023-03-17 22:54:25,239] [INFO] Running command: cat /var/lib/cwl/stgd43015f3-8af4-49d0-94a7-0fafed5c1461/OceanDNA-b28641.fa | prodigal -d OceanDNA-b28641/cds.fna -a OceanDNA-b28641/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:54:40,615] [INFO] Task succeeded: Prodigal
[2023-03-17 22:54:40,615] [INFO] Task started: HMMsearch
[2023-03-17 22:54:40,615] [INFO] Running command: hmmsearch --tblout OceanDNA-b28641/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca7d0b72-6c9c-4a30-9954-7eb112482110/dqc_reference/reference_markers.hmm OceanDNA-b28641/protein.faa > /dev/null
[2023-03-17 22:54:40,807] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:54:40,807] [INFO] Found 6/6 markers.
[2023-03-17 22:54:40,825] [INFO] Query marker FASTA was written to OceanDNA-b28641/markers.fasta
[2023-03-17 22:54:40,826] [INFO] Task started: Blastn
[2023-03-17 22:54:40,826] [INFO] Running command: blastn -query OceanDNA-b28641/markers.fasta -db /var/lib/cwl/stgca7d0b72-6c9c-4a30-9954-7eb112482110/dqc_reference/reference_markers.fasta -out OceanDNA-b28641/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:54:41,458] [INFO] Task succeeded: Blastn
[2023-03-17 22:54:41,459] [INFO] Selected 34 target genomes.
[2023-03-17 22:54:41,460] [INFO] Target genome list was writen to OceanDNA-b28641/target_genomes.txt
[2023-03-17 22:54:41,476] [INFO] Task started: fastANI
[2023-03-17 22:54:41,476] [INFO] Running command: fastANI --query /var/lib/cwl/stgd43015f3-8af4-49d0-94a7-0fafed5c1461/OceanDNA-b28641.fa --refList OceanDNA-b28641/target_genomes.txt --output OceanDNA-b28641/fastani_result.tsv --threads 1
[2023-03-17 22:55:01,700] [INFO] Task succeeded: fastANI
[2023-03-17 22:55:01,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca7d0b72-6c9c-4a30-9954-7eb112482110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:55:01,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca7d0b72-6c9c-4a30-9954-7eb112482110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:55:01,715] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:55:01,715] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:55:01,715] [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
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.3422	51	837	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.318	78	837	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.2579	66	837	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.1329	66	837	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.1058	71	837	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.102	69	837	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	76.0515	61	837	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.0157	60	837	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	76.0092	66	837	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	75.9937	52	837	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	75.9864	60	837	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	75.9376	59	837	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	75.9243	61	837	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	75.8991	66	837	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	75.8983	66	837	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	75.8951	59	837	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	75.8253	53	837	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	75.8049	51	837	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	75.7946	61	837	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	75.7757	66	837	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	75.7019	60	837	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	75.7015	56	837	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	75.5429	55	837	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	75.5334	55	837	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	75.5288	56	837	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	75.5224	60	837	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:55:01,716] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28641/tc_result.tsv
[2023-03-17 22:55:01,716] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:55:01,716] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:55:01,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca7d0b72-6c9c-4a30-9954-7eb112482110/dqc_reference/checkm_data
[2023-03-17 22:55:01,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:55:01,780] [INFO] Task started: CheckM
[2023-03-17 22:55:01,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28641/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28641/checkm_input OceanDNA-b28641/checkm_result
[2023-03-17 22:55:43,148] [INFO] Task succeeded: CheckM
[2023-03-17 22:55:43,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:55:43,152] [INFO] ===== Completeness check finished =====
[2023-03-17 22:55:43,152] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:55:43,152] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28641/markers.fasta)
[2023-03-17 22:55:43,153] [INFO] Task started: Blastn
[2023-03-17 22:55:43,153] [INFO] Running command: blastn -query OceanDNA-b28641/markers.fasta -db /var/lib/cwl/stgca7d0b72-6c9c-4a30-9954-7eb112482110/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28641/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:55:44,408] [INFO] Task succeeded: Blastn
[2023-03-17 22:55:44,409] [INFO] Selected 22 target genomes.
[2023-03-17 22:55:44,410] [INFO] Target genome list was writen to OceanDNA-b28641/target_genomes_gtdb.txt
[2023-03-17 22:55:44,458] [INFO] Task started: fastANI
[2023-03-17 22:55:44,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgd43015f3-8af4-49d0-94a7-0fafed5c1461/OceanDNA-b28641.fa --refList OceanDNA-b28641/target_genomes_gtdb.txt --output OceanDNA-b28641/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:55:57,785] [INFO] Task succeeded: fastANI
[2023-03-17 22:55:57,796] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:55:57,796] [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_002726375.1	s__CABZJG01 sp002726375	91.0101	498	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.70	96.98	0.64	0.64	3	-
GCA_902525995.1	s__CABZJG01 sp902525995	89.8415	342	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512685.1	s__CABZJG01 sp902512685	85.7393	444	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.75	97.42	0.59	0.54	7	-
GCA_001642945.1	s__LGRT01 sp001642945	76.9465	120	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	-
GCA_001510135.1	s__LFER01 sp001510135	76.7547	68	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LFER01	95.0	98.63	96.26	0.85	0.78	7	-
GCF_900115165.1	s__Roseovarius lutimaris	76.3009	75	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	76.1784	51	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	76.0704	70	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	76.0629	65	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458415.1	s__Epibacterium multivorans	76.0117	59	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900109035.1	s__Cribrihabitans marinus	76.0047	57	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900172335.1	s__Roseovarius albus	75.9963	59	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923355.1	s__Phaeobacter_A marinintestinus	75.9683	65	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	75.8548	59	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003014475.1	s__Shimia abyssi	75.7997	52	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	75.7015	56	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	75.6482	73	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_013317235.1	s__Leisingera sp013317235	75.5927	61	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001730095.1	s__Leisingera sp001730095	75.5758	71	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803475.1	s__Aliishimia ponticola	75.5713	53	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:55:57,797] [INFO] GTDB search result was written to OceanDNA-b28641/result_gtdb.tsv
[2023-03-17 22:55:57,797] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:55:57,800] [INFO] DFAST_QC result json was written to OceanDNA-b28641/dqc_result.json
[2023-03-17 22:55:57,800] [INFO] DFAST_QC completed!
[2023-03-17 22:55:57,800] [INFO] Total running time: 0h1m34s