[2023-03-18 21:30:55,921] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:30:55,921] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:30:55,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg279140e0-3146-4a58-b0dc-b808b405c013/dqc_reference
[2023-03-18 21:30:56,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:30:56,996] [INFO] Task started: Prodigal
[2023-03-18 21:30:56,996] [INFO] Running command: cat /var/lib/cwl/stg8dec9c80-001f-407d-bc7a-dacb847e3f0c/OceanDNA-b7466.fa | prodigal -d OceanDNA-b7466/cds.fna -a OceanDNA-b7466/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:31:15,533] [INFO] Task succeeded: Prodigal
[2023-03-18 21:31:15,533] [INFO] Task started: HMMsearch
[2023-03-18 21:31:15,533] [INFO] Running command: hmmsearch --tblout OceanDNA-b7466/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg279140e0-3146-4a58-b0dc-b808b405c013/dqc_reference/reference_markers.hmm OceanDNA-b7466/protein.faa > /dev/null
[2023-03-18 21:31:15,716] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:31:15,716] [INFO] Found 6/6 markers.
[2023-03-18 21:31:15,735] [INFO] Query marker FASTA was written to OceanDNA-b7466/markers.fasta
[2023-03-18 21:31:15,736] [INFO] Task started: Blastn
[2023-03-18 21:31:15,736] [INFO] Running command: blastn -query OceanDNA-b7466/markers.fasta -db /var/lib/cwl/stg279140e0-3146-4a58-b0dc-b808b405c013/dqc_reference/reference_markers.fasta -out OceanDNA-b7466/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:31:16,324] [INFO] Task succeeded: Blastn
[2023-03-18 21:31:16,325] [INFO] Selected 27 target genomes.
[2023-03-18 21:31:16,326] [INFO] Target genome list was writen to OceanDNA-b7466/target_genomes.txt
[2023-03-18 21:31:16,337] [INFO] Task started: fastANI
[2023-03-18 21:31:16,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dec9c80-001f-407d-bc7a-dacb847e3f0c/OceanDNA-b7466.fa --refList OceanDNA-b7466/target_genomes.txt --output OceanDNA-b7466/fastani_result.tsv --threads 1
[2023-03-18 21:31:31,138] [INFO] Task succeeded: fastANI
[2023-03-18 21:31:31,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg279140e0-3146-4a58-b0dc-b808b405c013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:31:31,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg279140e0-3146-4a58-b0dc-b808b405c013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:31:31,153] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:31:31,153] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:31:31,153] [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	77.7155	211	962	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.8762	118	962	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.8564	123	962	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.7312	117	962	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	76.7231	129	962	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	76.715	124	962	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.689	129	962	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	76.6711	93	962	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.6579	87	962	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	76.6456	128	962	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	76.6148	176	962	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	76.5911	86	962	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.5819	146	962	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.5764	106	962	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	76.5699	79	962	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.5553	130	962	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.5517	116	962	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.5444	102	962	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.5407	130	962	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.4331	147	962	95	below_threshold
Flavicella marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	76.3994	98	962	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.3809	145	962	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.2923	105	962	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.1445	114	962	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.0008	73	962	95	below_threshold
Tenacibaculum agarivorans	strain=HZ1	GCA_001936575.1	1908389	1908389	type	True	75.7537	80	962	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:31:31,153] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7466/tc_result.tsv
[2023-03-18 21:31:31,153] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:31:31,153] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:31:31,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg279140e0-3146-4a58-b0dc-b808b405c013/dqc_reference/checkm_data
[2023-03-18 21:31:31,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:31:31,159] [INFO] Task started: CheckM
[2023-03-18 21:31:31,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7466/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7466/checkm_input OceanDNA-b7466/checkm_result
[2023-03-18 21:32:18,829] [INFO] Task succeeded: CheckM
[2023-03-18 21:32:18,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:32:18,832] [INFO] ===== Completeness check finished =====
[2023-03-18 21:32:18,832] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:32:18,832] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7466/markers.fasta)
[2023-03-18 21:32:18,833] [INFO] Task started: Blastn
[2023-03-18 21:32:18,833] [INFO] Running command: blastn -query OceanDNA-b7466/markers.fasta -db /var/lib/cwl/stg279140e0-3146-4a58-b0dc-b808b405c013/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7466/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:32:19,666] [INFO] Task succeeded: Blastn
[2023-03-18 21:32:19,667] [INFO] Selected 20 target genomes.
[2023-03-18 21:32:19,667] [INFO] Target genome list was writen to OceanDNA-b7466/target_genomes_gtdb.txt
[2023-03-18 21:32:19,703] [INFO] Task started: fastANI
[2023-03-18 21:32:19,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dec9c80-001f-407d-bc7a-dacb847e3f0c/OceanDNA-b7466.fa --refList OceanDNA-b7466/target_genomes_gtdb.txt --output OceanDNA-b7466/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:32:31,400] [INFO] Task succeeded: fastANI
[2023-03-18 21:32:31,412] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:32:31,412] [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_905181865.1	s__Urechidicola croceus_A	99.7456	908	962	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_016744415.1	s__Urechidicola sp016744415	77.7454	181	962	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	77.7154	211	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874265.1	s__Urechidicola sp001874265	77.6881	212	962	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	77.3807	151	962	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	77.3122	117	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	76.9699	135	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	76.7522	141	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543325.1	s__Lutibacter profundi	76.715	124	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006381105.1	s__Flavicella sediminum	76.6278	129	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	76.614	139	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	76.5584	102	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004121075.1	s__Lutibacter sp004121075	76.5255	145	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106565.1	s__Lutibacter oricola	76.3837	146	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054895.1	s__Lutibacter sp018054895	76.3198	111	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	76.3154	105	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_001975665.1	s__Polaribacter reichenbachii	76.2838	114	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCA_002401385.1	s__GCA-002401385 sp002401385	76.1817	56	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002401385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	76.1726	151	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744615.1	s__QNYL01 sp016744615	75.6777	68	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__QNYL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:32:31,412] [INFO] GTDB search result was written to OceanDNA-b7466/result_gtdb.tsv
[2023-03-18 21:32:31,412] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:32:31,414] [INFO] DFAST_QC result json was written to OceanDNA-b7466/dqc_result.json
[2023-03-18 21:32:31,415] [INFO] DFAST_QC completed!
[2023-03-18 21:32:31,415] [INFO] Total running time: 0h1m35s