[2023-03-17 02:31:12,849] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,849] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,849] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5fd0736-2850-4872-9b20-f4bc6d969354/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,378] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,378] [INFO] Running command: cat /var/lib/cwl/stg9025f7cf-c283-4078-99cf-e9659422da04/OceanDNA-b11400.fa | prodigal -d OceanDNA-b11400/cds.fna -a OceanDNA-b11400/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:29,907] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:29,908] [INFO] Task started: HMMsearch
[2023-03-17 02:31:29,908] [INFO] Running command: hmmsearch --tblout OceanDNA-b11400/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5fd0736-2850-4872-9b20-f4bc6d969354/dqc_reference/reference_markers.hmm OceanDNA-b11400/protein.faa > /dev/null
[2023-03-17 02:31:30,091] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:30,092] [INFO] Found 6/6 markers.
[2023-03-17 02:31:30,108] [INFO] Query marker FASTA was written to OceanDNA-b11400/markers.fasta
[2023-03-17 02:31:30,109] [INFO] Task started: Blastn
[2023-03-17 02:31:30,109] [INFO] Running command: blastn -query OceanDNA-b11400/markers.fasta -db /var/lib/cwl/stgb5fd0736-2850-4872-9b20-f4bc6d969354/dqc_reference/reference_markers.fasta -out OceanDNA-b11400/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:30,720] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:30,721] [INFO] Selected 19 target genomes.
[2023-03-17 02:31:30,721] [INFO] Target genome list was writen to OceanDNA-b11400/target_genomes.txt
[2023-03-17 02:31:30,729] [INFO] Task started: fastANI
[2023-03-17 02:31:30,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg9025f7cf-c283-4078-99cf-e9659422da04/OceanDNA-b11400.fa --refList OceanDNA-b11400/target_genomes.txt --output OceanDNA-b11400/fastani_result.tsv --threads 1
[2023-03-17 02:31:44,275] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:44,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5fd0736-2850-4872-9b20-f4bc6d969354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:44,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5fd0736-2850-4872-9b20-f4bc6d969354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:44,287] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:44,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:31:44,287] [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 echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.4311	461	860	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.4296	462	860	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	79.3981	410	860	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	79.321	417	860	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	79.2497	428	860	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	79.1775	411	860	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	79.1272	424	860	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	79.1243	406	860	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	79.0773	399	860	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	79.0252	403	860	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	79.0112	383	860	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.8721	403	860	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.7342	387	860	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	78.5734	371	860	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.437	185	860	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.2796	164	860	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.2643	163	860	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.2294	215	860	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.0293	84	860	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:31:44,287] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11400/tc_result.tsv
[2023-03-17 02:31:44,287] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:44,287] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:44,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5fd0736-2850-4872-9b20-f4bc6d969354/dqc_reference/checkm_data
[2023-03-17 02:31:44,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:44,292] [INFO] Task started: CheckM
[2023-03-17 02:31:44,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11400/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11400/checkm_input OceanDNA-b11400/checkm_result
[2023-03-17 02:32:24,904] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:24,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:32:24,906] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:24,907] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:24,907] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11400/markers.fasta)
[2023-03-17 02:32:24,908] [INFO] Task started: Blastn
[2023-03-17 02:32:24,908] [INFO] Running command: blastn -query OceanDNA-b11400/markers.fasta -db /var/lib/cwl/stgb5fd0736-2850-4872-9b20-f4bc6d969354/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11400/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:25,750] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:25,751] [INFO] Selected 15 target genomes.
[2023-03-17 02:32:25,751] [INFO] Target genome list was writen to OceanDNA-b11400/target_genomes_gtdb.txt
[2023-03-17 02:32:25,969] [INFO] Task started: fastANI
[2023-03-17 02:32:25,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg9025f7cf-c283-4078-99cf-e9659422da04/OceanDNA-b11400.fa --refList OceanDNA-b11400/target_genomes_gtdb.txt --output OceanDNA-b11400/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:36,530] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:36,539] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:32:36,539] [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_002364335.1	s__Winogradskyella sp002364335	81.2791	579	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	79.6296	438	860	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	79.4296	462	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013285155.1	s__Winogradskyella undariae	79.344	415	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	79.2501	425	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	79.2384	429	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	79.227	443	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	79.1762	412	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	79.1492	422	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	79.1242	407	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	79.0971	401	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_013403925.1	s__Winogradskyella wichelsiae	79.0223	383	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	78.9844	390	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	78.9046	436	860	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	77.7695	279	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:32:36,539] [INFO] GTDB search result was written to OceanDNA-b11400/result_gtdb.tsv
[2023-03-17 02:32:36,539] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:36,541] [INFO] DFAST_QC result json was written to OceanDNA-b11400/dqc_result.json
[2023-03-17 02:32:36,541] [INFO] DFAST_QC completed!
[2023-03-17 02:32:36,542] [INFO] Total running time: 0h1m24s