[2024-01-24 12:06:50,973] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a1d7eca-9c62-4152-8e92-fb90eb947251/dqc_reference
[2024-01-24 12:06:52,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:52,157] [INFO] Task started: Prodigal
[2024-01-24 12:06:52,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg23973ed5-33f9-4741-9529-ff6b0162d6c1/GCF_002217435.1_ASM221743v1_genomic.fna.gz | prodigal -d GCF_002217435.1_ASM221743v1_genomic.fna/cds.fna -a GCF_002217435.1_ASM221743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:10,130] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:10,131] [INFO] Task started: HMMsearch
[2024-01-24 12:07:10,131] [INFO] Running command: hmmsearch --tblout GCF_002217435.1_ASM221743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a1d7eca-9c62-4152-8e92-fb90eb947251/dqc_reference/reference_markers.hmm GCF_002217435.1_ASM221743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:10,419] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:10,421] [INFO] Found 6/6 markers.
[2024-01-24 12:07:10,468] [INFO] Query marker FASTA was written to GCF_002217435.1_ASM221743v1_genomic.fna/markers.fasta
[2024-01-24 12:07:10,469] [INFO] Task started: Blastn
[2024-01-24 12:07:10,469] [INFO] Running command: blastn -query GCF_002217435.1_ASM221743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a1d7eca-9c62-4152-8e92-fb90eb947251/dqc_reference/reference_markers.fasta -out GCF_002217435.1_ASM221743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:11,162] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:11,166] [INFO] Selected 24 target genomes.
[2024-01-24 12:07:11,167] [INFO] Target genome list was writen to GCF_002217435.1_ASM221743v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:11,178] [INFO] Task started: fastANI
[2024-01-24 12:07:11,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg23973ed5-33f9-4741-9529-ff6b0162d6c1/GCF_002217435.1_ASM221743v1_genomic.fna.gz --refList GCF_002217435.1_ASM221743v1_genomic.fna/target_genomes.txt --output GCF_002217435.1_ASM221743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:38,161] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:38,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a1d7eca-9c62-4152-8e92-fb90eb947251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:38,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a1d7eca-9c62-4152-8e92-fb90eb947251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:38,185] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:38,185] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:38,185] [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 reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	100.0	1828	1831	95	conclusive
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.1741	1030	1831	95	below_threshold
Flavobacterium panici		GCA_903819335.1	2654843	2654843	type	True	83.1171	1128	1831	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.7678	1149	1831	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	82.6763	1103	1831	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	82.672	1146	1831	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	82.6619	961	1831	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	82.6552	1147	1831	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	82.6173	955	1831	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	82.6078	1161	1831	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	82.5988	1077	1831	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	82.5091	1044	1831	95	below_threshold
Flavobacterium chungbukense	strain=CS100	GCA_020805785.1	877464	877464	type	True	82.5039	1121	1831	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	82.4843	1107	1831	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	82.3949	1083	1831	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	82.3818	1076	1831	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	82.14	1083	1831	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	82.0618	969	1831	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.9724	1087	1831	95	below_threshold
Flavobacterium circumlabens	strain=P5626	GCA_004345565.1	2133765	2133765	type	True	81.7751	1044	1831	95	below_threshold
Flavobacterium circumlabens	strain=CCM 8828	GCA_004369705.1	2133765	2133765	type	True	81.7538	1048	1831	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	81.595	902	1831	95	below_threshold
Flavobacterium cupreum	strain=CCM 8825	GCA_003996965.1	2133766	2133766	type	True	81.4205	1026	1831	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.7164	154	1831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:38,187] [INFO] DFAST Taxonomy check result was written to GCF_002217435.1_ASM221743v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:38,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:38,188] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:38,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a1d7eca-9c62-4152-8e92-fb90eb947251/dqc_reference/checkm_data
[2024-01-24 12:07:38,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:38,246] [INFO] Task started: CheckM
[2024-01-24 12:07:38,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217435.1_ASM221743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217435.1_ASM221743v1_genomic.fna/checkm_input GCF_002217435.1_ASM221743v1_genomic.fna/checkm_result
[2024-01-24 12:08:30,835] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:30,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:30,861] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:30,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:30,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217435.1_ASM221743v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:30,862] [INFO] Task started: Blastn
[2024-01-24 12:08:30,862] [INFO] Running command: blastn -query GCF_002217435.1_ASM221743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a1d7eca-9c62-4152-8e92-fb90eb947251/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217435.1_ASM221743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:31,797] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:31,800] [INFO] Selected 21 target genomes.
[2024-01-24 12:08:31,800] [INFO] Target genome list was writen to GCF_002217435.1_ASM221743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:31,816] [INFO] Task started: fastANI
[2024-01-24 12:08:31,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg23973ed5-33f9-4741-9529-ff6b0162d6c1/GCF_002217435.1_ASM221743v1_genomic.fna.gz --refList GCF_002217435.1_ASM221743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217435.1_ASM221743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:56,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:56,976] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:56,976] [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_002217435.1	s__Flavobacterium reichenbachii	100.0	1828	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_004368785.1	s__Flavobacterium sp004368785	83.9602	1218	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711165.2	s__Flavobacterium sp009711165	83.1996	1201	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428525.1	s__Flavobacterium sp001428525	83.0905	1142	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210235.1	s__Flavobacterium sp002210235	83.0794	1137	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCF_900129795.1	s__Flavobacterium sp900129795	83.005	1130	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_009711135.1	s__Flavobacterium sp009711135	82.9899	1075	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707955.1	s__Flavobacterium sp009707955	82.9023	1141	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001422725.1	s__Flavobacterium sp001422725	82.8965	1118	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482975.1	s__Flavobacterium sp002482975	82.8894	1112	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833415.1	s__Flavobacterium sp017833415	82.8077	1084	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001507425.1	s__Flavobacterium sp001507425	82.7967	1153	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362055.1	s__Flavobacterium sp004362055	82.6957	1033	1831	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	82.6714	1078	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	82.6676	961	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	82.6129	1160	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_902804475.1	s__Flavobacterium bizetiae	82.5169	1043	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCF_018380615.1	s__Flavobacterium psychroterrae	82.4894	1105	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345565.1	s__Flavobacterium circumlabens	81.7778	1043	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.60	96.60	0.85	0.85	2	-
GCF_009674775.1	s__Flavobacterium sp009674775	81.6991	990	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217285.1	s__Flavobacterium hercynium	81.568	906	1831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:56,978] [INFO] GTDB search result was written to GCF_002217435.1_ASM221743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:56,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:56,985] [INFO] DFAST_QC result json was written to GCF_002217435.1_ASM221743v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:56,986] [INFO] DFAST_QC completed!
[2024-01-24 12:08:56,986] [INFO] Total running time: 0h2m6s