[2023-03-17 00:45:47,257] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,257] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,257] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc564e8c-12ff-43c0-be72-5d43e9dd08e5/dqc_reference
[2023-03-17 00:45:48,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,377] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,378] [INFO] Running command: cat /var/lib/cwl/stgf7056fe4-aaee-4640-bf9a-ba4c2b944ee3/OceanDNA-b6771.fa | prodigal -d OceanDNA-b6771/cds.fna -a OceanDNA-b6771/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:23,250] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:23,250] [INFO] Task started: HMMsearch
[2023-03-17 00:46:23,250] [INFO] Running command: hmmsearch --tblout OceanDNA-b6771/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc564e8c-12ff-43c0-be72-5d43e9dd08e5/dqc_reference/reference_markers.hmm OceanDNA-b6771/protein.faa > /dev/null
[2023-03-17 00:46:23,485] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:23,485] [INFO] Found 6/6 markers.
[2023-03-17 00:46:23,515] [INFO] Query marker FASTA was written to OceanDNA-b6771/markers.fasta
[2023-03-17 00:46:23,516] [INFO] Task started: Blastn
[2023-03-17 00:46:23,517] [INFO] Running command: blastn -query OceanDNA-b6771/markers.fasta -db /var/lib/cwl/stgfc564e8c-12ff-43c0-be72-5d43e9dd08e5/dqc_reference/reference_markers.fasta -out OceanDNA-b6771/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:24,147] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:24,148] [INFO] Selected 21 target genomes.
[2023-03-17 00:46:24,148] [INFO] Target genome list was writen to OceanDNA-b6771/target_genomes.txt
[2023-03-17 00:46:24,158] [INFO] Task started: fastANI
[2023-03-17 00:46:24,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7056fe4-aaee-4640-bf9a-ba4c2b944ee3/OceanDNA-b6771.fa --refList OceanDNA-b6771/target_genomes.txt --output OceanDNA-b6771/fastani_result.tsv --threads 1
[2023-03-17 00:46:47,312] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:47,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc564e8c-12ff-43c0-be72-5d43e9dd08e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:47,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc564e8c-12ff-43c0-be72-5d43e9dd08e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:47,324] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 00:46:47,324] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 00:46:47,324] [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
Flavobacterium collinsii		GCA_902804485.1	1114861	1114861	type	True	97.9242	1493	1789	95	conclusive
Flavobacterium tructae	strain=CCUG 60100	GCA_002217475.1	1114873	1114873	type	True	88.2828	1242	1789	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	83.372	1025	1789	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	83.3717	1027	1789	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	83.3396	977	1789	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	83.1737	1005	1789	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	83.1056	1076	1789	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	83.1055	995	1789	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	83.0972	985	1789	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	83.0781	1002	1789	95	below_threshold
Flavobacterium chilense	strain=DSM 24724	GCA_900142685.1	946677	946677	type	True	83.0655	1078	1789	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	83.0183	1040	1789	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.09	877	1789	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	82.0822	900	1789	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	82.0273	920	1789	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	81.7876	815	1789	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.1317	825	1789	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	81.1103	726	1789	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.1032	833	1789	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	80.9403	856	1789	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.1667	148	1789	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:47,324] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6771/tc_result.tsv
[2023-03-17 00:46:47,324] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:47,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:47,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc564e8c-12ff-43c0-be72-5d43e9dd08e5/dqc_reference/checkm_data
[2023-03-17 00:46:47,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:47,332] [INFO] Task started: CheckM
[2023-03-17 00:46:47,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6771/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6771/checkm_input OceanDNA-b6771/checkm_result
[2023-03-17 00:48:10,864] [INFO] Task succeeded: CheckM
[2023-03-17 00:48:10,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:48:10,867] [INFO] ===== Completeness check finished =====
[2023-03-17 00:48:10,867] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:48:10,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6771/markers.fasta)
[2023-03-17 00:48:10,869] [INFO] Task started: Blastn
[2023-03-17 00:48:10,869] [INFO] Running command: blastn -query OceanDNA-b6771/markers.fasta -db /var/lib/cwl/stgfc564e8c-12ff-43c0-be72-5d43e9dd08e5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6771/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:48:11,776] [INFO] Task succeeded: Blastn
[2023-03-17 00:48:11,777] [INFO] Selected 19 target genomes.
[2023-03-17 00:48:11,777] [INFO] Target genome list was writen to OceanDNA-b6771/target_genomes_gtdb.txt
[2023-03-17 00:48:12,077] [INFO] Task started: fastANI
[2023-03-17 00:48:12,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7056fe4-aaee-4640-bf9a-ba4c2b944ee3/OceanDNA-b6771.fa --refList OceanDNA-b6771/target_genomes_gtdb.txt --output OceanDNA-b6771/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:48:34,624] [INFO] Task succeeded: fastANI
[2023-03-17 00:48:34,634] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:48:34,635] [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
GCF_902804485.1	s__Flavobacterium collinsii	97.9172	1494	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002217475.1	s__Flavobacterium tructae	88.2828	1242	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.59	96.94	0.94	0.93	4	-
GCF_903469665.1	s__Flavobacterium sp903469665	88.059	1237	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664855.1	s__Flavobacterium sp009664855	83.3795	999	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.90	98.90	0.89	0.89	2	-
GCF_902804475.1	s__Flavobacterium bizetiae	83.3454	977	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCA_900129595.1	s__Flavobacterium frigidimaris	83.3082	1044	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001975985.1	s__Flavobacterium sp001975985	83.2585	984	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001602525.1	s__Flavobacterium chilense	83.1023	1076	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.61	0.93	0.86	3	-
GCF_001686925.1	s__Flavobacterium piscis	83.0919	1000	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_001422725.1	s__Flavobacterium sp001422725	83.075	1020	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754195.1	s__Flavobacterium sp002754195	83.0512	1088	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832125.1	s__Flavobacterium hibernum	83.0277	1009	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_004339525.1	s__Flavobacterium sp004339525	82.9833	1092	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	82.9023	1060	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362015.1	s__Flavobacterium sp004362015	82.1487	901	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217395.1	s__Flavobacterium plurextorum	82.011	922	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
GCF_009711135.1	s__Flavobacterium sp009711135	82.0062	895	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004368785.1	s__Flavobacterium sp004368785	81.6589	883	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002304005.1	s__Flavobacterium sp002304005	81.6524	829	1789	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:48:34,635] [INFO] GTDB search result was written to OceanDNA-b6771/result_gtdb.tsv
[2023-03-17 00:48:34,635] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:48:34,637] [INFO] DFAST_QC result json was written to OceanDNA-b6771/dqc_result.json
[2023-03-17 00:48:34,637] [INFO] DFAST_QC completed!
[2023-03-17 00:48:34,637] [INFO] Total running time: 0h2m47s