[2023-03-15 08:11:05,964] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:11:05,964] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:11:05,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg271c0248-04a3-40be-b51f-9388b9c6b991/dqc_reference
[2023-03-15 08:11:07,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:11:07,058] [INFO] Task started: Prodigal
[2023-03-15 08:11:07,058] [INFO] Running command: cat /var/lib/cwl/stg0f936c17-db62-4808-beff-8ca3add88e0a/OceanDNA-b7546.fa | prodigal -d OceanDNA-b7546/cds.fna -a OceanDNA-b7546/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:11:23,255] [INFO] Task succeeded: Prodigal
[2023-03-15 08:11:23,255] [INFO] Task started: HMMsearch
[2023-03-15 08:11:23,255] [INFO] Running command: hmmsearch --tblout OceanDNA-b7546/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg271c0248-04a3-40be-b51f-9388b9c6b991/dqc_reference/reference_markers.hmm OceanDNA-b7546/protein.faa > /dev/null
[2023-03-15 08:11:23,473] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:11:23,473] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0f936c17-db62-4808-beff-8ca3add88e0a/OceanDNA-b7546.fa]
[2023-03-15 08:11:23,500] [INFO] Query marker FASTA was written to OceanDNA-b7546/markers.fasta
[2023-03-15 08:11:23,501] [INFO] Task started: Blastn
[2023-03-15 08:11:23,501] [INFO] Running command: blastn -query OceanDNA-b7546/markers.fasta -db /var/lib/cwl/stg271c0248-04a3-40be-b51f-9388b9c6b991/dqc_reference/reference_markers.fasta -out OceanDNA-b7546/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:24,109] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:24,110] [INFO] Selected 14 target genomes.
[2023-03-15 08:11:24,110] [INFO] Target genome list was writen to OceanDNA-b7546/target_genomes.txt
[2023-03-15 08:11:24,119] [INFO] Task started: fastANI
[2023-03-15 08:11:24,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f936c17-db62-4808-beff-8ca3add88e0a/OceanDNA-b7546.fa --refList OceanDNA-b7546/target_genomes.txt --output OceanDNA-b7546/fastani_result.tsv --threads 1
[2023-03-15 08:11:32,850] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:32,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg271c0248-04a3-40be-b51f-9388b9c6b991/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:11:32,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg271c0248-04a3-40be-b51f-9388b9c6b991/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:11:32,860] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:11:32,860] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:11:32,860] [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
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	79.9626	475	861	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	79.8955	525	861	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	79.7526	517	861	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	79.7211	524	861	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	79.4508	507	861	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	79.2878	445	861	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	79.1567	438	861	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	78.9556	426	861	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.9265	173	861	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.8403	208	861	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	76.8287	196	861	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.6107	174	861	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.4934	163	861	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.0959	86	861	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:11:32,866] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7546/tc_result.tsv
[2023-03-15 08:11:32,866] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:11:32,866] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:11:32,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg271c0248-04a3-40be-b51f-9388b9c6b991/dqc_reference/checkm_data
[2023-03-15 08:11:32,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:11:32,879] [INFO] Task started: CheckM
[2023-03-15 08:11:32,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7546/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7546/checkm_input OceanDNA-b7546/checkm_result
[2023-03-15 08:12:15,767] [INFO] Task succeeded: CheckM
[2023-03-15 08:12:15,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:12:15,824] [INFO] ===== Completeness check finished =====
[2023-03-15 08:12:15,824] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:12:15,824] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7546/markers.fasta)
[2023-03-15 08:12:15,825] [INFO] Task started: Blastn
[2023-03-15 08:12:15,825] [INFO] Running command: blastn -query OceanDNA-b7546/markers.fasta -db /var/lib/cwl/stg271c0248-04a3-40be-b51f-9388b9c6b991/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7546/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:12:16,709] [INFO] Task succeeded: Blastn
[2023-03-15 08:12:16,723] [INFO] Selected 12 target genomes.
[2023-03-15 08:12:16,723] [INFO] Target genome list was writen to OceanDNA-b7546/target_genomes_gtdb.txt
[2023-03-15 08:12:16,735] [INFO] Task started: fastANI
[2023-03-15 08:12:16,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f936c17-db62-4808-beff-8ca3add88e0a/OceanDNA-b7546.fa --refList OceanDNA-b7546/target_genomes_gtdb.txt --output OceanDNA-b7546/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:12:24,381] [INFO] Task succeeded: fastANI
[2023-03-15 08:12:24,388] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:12:24,388] [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_004195315.1	s__Lutibacter sp004195315	85.3562	387	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	82.6034	517	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	80.7612	500	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001543325.1	s__Lutibacter profundi	79.9676	476	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733285.1	s__Lutibacter sp002733285	79.9231	422	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	97.79	97.79	0.89	0.89	2	-
GCA_016342705.1	s__Lutibacter sp016342705	79.9167	501	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188355.1	s__Lutibacter flavus	79.8842	525	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	79.7253	521	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014646675.1	s__Lutibacter litoralis	79.5112	473	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260195.1	s__Lutibacter citreus	79.1567	438	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015767395.1	s__Lutibacter sp015767395	78.9134	285	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524075.1	s__Lutibacter sp012524075	78.8389	406	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:12:24,397] [INFO] GTDB search result was written to OceanDNA-b7546/result_gtdb.tsv
[2023-03-15 08:12:24,402] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:12:24,412] [INFO] DFAST_QC result json was written to OceanDNA-b7546/dqc_result.json
[2023-03-15 08:12:24,412] [INFO] DFAST_QC completed!
[2023-03-15 08:12:24,412] [INFO] Total running time: 0h1m18s