[2023-03-15 23:42:29,663] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,663] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg621eda07-07ae-43f0-9b3d-f8abc9c2273d/dqc_reference
[2023-03-15 23:42:31,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,276] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,276] [INFO] Running command: cat /var/lib/cwl/stg62f72366-4e2b-4ed9-a6f3-dc683a7e7762/OceanDNA-b7469.fa | prodigal -d OceanDNA-b7469/cds.fna -a OceanDNA-b7469/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:47,116] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:47,117] [INFO] Task started: HMMsearch
[2023-03-15 23:42:47,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b7469/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg621eda07-07ae-43f0-9b3d-f8abc9c2273d/dqc_reference/reference_markers.hmm OceanDNA-b7469/protein.faa > /dev/null
[2023-03-15 23:42:47,307] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:47,308] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg62f72366-4e2b-4ed9-a6f3-dc683a7e7762/OceanDNA-b7469.fa]
[2023-03-15 23:42:47,324] [INFO] Query marker FASTA was written to OceanDNA-b7469/markers.fasta
[2023-03-15 23:42:47,325] [INFO] Task started: Blastn
[2023-03-15 23:42:47,325] [INFO] Running command: blastn -query OceanDNA-b7469/markers.fasta -db /var/lib/cwl/stg621eda07-07ae-43f0-9b3d-f8abc9c2273d/dqc_reference/reference_markers.fasta -out OceanDNA-b7469/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:47,914] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:47,915] [INFO] Selected 21 target genomes.
[2023-03-15 23:42:47,915] [INFO] Target genome list was writen to OceanDNA-b7469/target_genomes.txt
[2023-03-15 23:42:47,929] [INFO] Task started: fastANI
[2023-03-15 23:42:47,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg62f72366-4e2b-4ed9-a6f3-dc683a7e7762/OceanDNA-b7469.fa --refList OceanDNA-b7469/target_genomes.txt --output OceanDNA-b7469/fastani_result.tsv --threads 1
[2023-03-15 23:42:58,985] [INFO] Task succeeded: fastANI
[2023-03-15 23:42:58,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg621eda07-07ae-43f0-9b3d-f8abc9c2273d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:42:58,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg621eda07-07ae-43f0-9b3d-f8abc9c2273d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:42:58,998] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:42:58,998] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:42:58,998] [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
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	77.5051	211	810	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.9977	139	810	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.8865	140	810	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.8272	140	810	95	below_threshold
Flavicella marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	76.8173	79	810	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.7379	145	810	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.7198	136	810	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.7172	139	810	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.6985	148	810	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.671	131	810	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.6701	139	810	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.6218	140	810	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.6114	139	810	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.5813	152	810	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	76.4432	129	810	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	76.3809	97	810	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	76.3647	99	810	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	76.3601	96	810	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.3396	107	810	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	76.2567	116	810	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.2194	96	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:42:58,998] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7469/tc_result.tsv
[2023-03-15 23:42:58,999] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:42:58,999] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:42:58,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg621eda07-07ae-43f0-9b3d-f8abc9c2273d/dqc_reference/checkm_data
[2023-03-15 23:42:58,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:42:59,012] [INFO] Task started: CheckM
[2023-03-15 23:42:59,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7469/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7469/checkm_input OceanDNA-b7469/checkm_result
[2023-03-15 23:43:40,937] [INFO] Task succeeded: CheckM
[2023-03-15 23:43:40,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:43:40,940] [INFO] ===== Completeness check finished =====
[2023-03-15 23:43:40,941] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:43:40,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7469/markers.fasta)
[2023-03-15 23:43:40,942] [INFO] Task started: Blastn
[2023-03-15 23:43:40,942] [INFO] Running command: blastn -query OceanDNA-b7469/markers.fasta -db /var/lib/cwl/stg621eda07-07ae-43f0-9b3d-f8abc9c2273d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7469/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:43:41,768] [INFO] Task succeeded: Blastn
[2023-03-15 23:43:41,769] [INFO] Selected 17 target genomes.
[2023-03-15 23:43:41,769] [INFO] Target genome list was writen to OceanDNA-b7469/target_genomes_gtdb.txt
[2023-03-15 23:43:41,781] [INFO] Task started: fastANI
[2023-03-15 23:43:41,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg62f72366-4e2b-4ed9-a6f3-dc683a7e7762/OceanDNA-b7469.fa --refList OceanDNA-b7469/target_genomes_gtdb.txt --output OceanDNA-b7469/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:43:50,804] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:50,814] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:43:50,814] [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_001874265.1	s__Urechidicola sp001874265	99.8305	740	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181865.1	s__Urechidicola croceus_A	78.0066	183	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401215.1	s__Urechidicola sp002401215	77.6014	115	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744415.1	s__Urechidicola sp016744415	77.5053	208	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761325.1	s__Urechidicola croceus	77.5051	211	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733665.1	s__Urechidicola sp002733665	77.1605	168	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	76.7195	139	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002163835.1	s__Polaribacter sp002163835	76.63	134	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	76.6059	141	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524075.1	s__Lutibacter sp012524075	76.5934	127	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	76.5813	152	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	76.4816	128	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	76.43	130	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003384935.1	s__Lutibacter oceani	76.3915	152	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003867075.1	s__Tenacibaculum mesophilum	76.3647	99	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCF_017498485.1	s__Polaribacter sp017498485	76.324	108	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867015.1	s__Tenacibaculum singaporense	76.2714	115	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 23:43:50,815] [INFO] GTDB search result was written to OceanDNA-b7469/result_gtdb.tsv
[2023-03-15 23:43:50,815] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:43:50,817] [INFO] DFAST_QC result json was written to OceanDNA-b7469/dqc_result.json
[2023-03-15 23:43:50,817] [INFO] DFAST_QC completed!
[2023-03-15 23:43:50,817] [INFO] Total running time: 0h1m21s