[2024-01-24 13:28:13,223] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,225] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg9519d5c6-39c1-4228-8ef7-d2ec3760dde6/dqc_reference
[2024-01-24 13:28:14,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,486] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cfb58e1-5c41-4f20-bcdf-19ceaff37448/GCF_903819435.1_CIP111411_genomic.fna.gz | prodigal -d GCF_903819435.1_CIP111411_genomic.fna/cds.fna -a GCF_903819435.1_CIP111411_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:35,056] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:35,057] [INFO] Task started: HMMsearch
[2024-01-24 13:28:35,057] [INFO] Running command: hmmsearch --tblout GCF_903819435.1_CIP111411_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9519d5c6-39c1-4228-8ef7-d2ec3760dde6/dqc_reference/reference_markers.hmm GCF_903819435.1_CIP111411_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:35,454] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:35,455] [INFO] Found 6/6 markers.
[2024-01-24 13:28:35,504] [INFO] Query marker FASTA was written to GCF_903819435.1_CIP111411_genomic.fna/markers.fasta
[2024-01-24 13:28:35,504] [INFO] Task started: Blastn
[2024-01-24 13:28:35,504] [INFO] Running command: blastn -query GCF_903819435.1_CIP111411_genomic.fna/markers.fasta -db /var/lib/cwl/stg9519d5c6-39c1-4228-8ef7-d2ec3760dde6/dqc_reference/reference_markers.fasta -out GCF_903819435.1_CIP111411_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:36,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:36,232] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:36,232] [INFO] Target genome list was writen to GCF_903819435.1_CIP111411_genomic.fna/target_genomes.txt
[2024-01-24 13:28:36,238] [INFO] Task started: fastANI
[2024-01-24 13:28:36,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cfb58e1-5c41-4f20-bcdf-19ceaff37448/GCF_903819435.1_CIP111411_genomic.fna.gz --refList GCF_903819435.1_CIP111411_genomic.fna/target_genomes.txt --output GCF_903819435.1_CIP111411_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:00,471] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:00,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9519d5c6-39c1-4228-8ef7-d2ec3760dde6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:00,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9519d5c6-39c1-4228-8ef7-d2ec3760dde6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:00,493] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:00,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:00,493] [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 salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	100.0	1911	1915	95	conclusive
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	86.3712	1288	1915	95	below_threshold
Flavobacterium cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	85.9943	1207	1915	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	85.2257	1196	1915	95	below_threshold
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	84.7585	1272	1915	95	below_threshold
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	84.7425	1267	1915	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	82.1286	1041	1915	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.1257	1063	1915	95	below_threshold
Flavobacterium frigidimaris	strain=DSM 15937	GCA_002217275.1	262320	262320	type	True	82.1149	952	1915	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	81.939	959	1915	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.9057	956	1915	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	81.7996	988	1915	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	81.6474	965	1915	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	81.6318	930	1915	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	81.6109	835	1915	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.46	862	1915	95	below_threshold
Flavobacterium collinsii		GCA_902804485.1	1114861	1114861	type	True	81.2724	801	1915	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.2205	926	1915	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.2126	932	1915	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.0696	173	1915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:00,495] [INFO] DFAST Taxonomy check result was written to GCF_903819435.1_CIP111411_genomic.fna/tc_result.tsv
[2024-01-24 13:29:00,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:00,496] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:00,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9519d5c6-39c1-4228-8ef7-d2ec3760dde6/dqc_reference/checkm_data
[2024-01-24 13:29:00,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:00,560] [INFO] Task started: CheckM
[2024-01-24 13:29:00,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_903819435.1_CIP111411_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_903819435.1_CIP111411_genomic.fna/checkm_input GCF_903819435.1_CIP111411_genomic.fna/checkm_result
[2024-01-24 13:29:57,508] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:57,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:57,535] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:57,535] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:57,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_903819435.1_CIP111411_genomic.fna/markers.fasta)
[2024-01-24 13:29:57,536] [INFO] Task started: Blastn
[2024-01-24 13:29:57,536] [INFO] Running command: blastn -query GCF_903819435.1_CIP111411_genomic.fna/markers.fasta -db /var/lib/cwl/stg9519d5c6-39c1-4228-8ef7-d2ec3760dde6/dqc_reference/reference_markers_gtdb.fasta -out GCF_903819435.1_CIP111411_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:58,536] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:58,540] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:58,541] [INFO] Target genome list was writen to GCF_903819435.1_CIP111411_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:58,561] [INFO] Task started: fastANI
[2024-01-24 13:29:58,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cfb58e1-5c41-4f20-bcdf-19ceaff37448/GCF_903819435.1_CIP111411_genomic.fna.gz --refList GCF_903819435.1_CIP111411_genomic.fna/target_genomes_gtdb.txt --output GCF_903819435.1_CIP111411_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:19,432] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:19,450] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:19,450] [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_000735715.2	s__Flavobacterium chungangense	95.2469	1539	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	conclusive
GCF_003202405.1	s__Flavobacterium hydrophilum	86.3474	1291	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202435.1	s__Flavobacterium cheongpyeongense	85.9975	1207	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645075.1	s__Flavobacterium limi	84.7533	1272	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010614725.1	s__Flavobacterium ajazii	84.738	1269	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645065.1	s__Flavobacterium fluviatile	84.5602	1065	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282055.1	s__Flavobacterium sp000282055	83.1616	1102	1915	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	82.314	1005	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000708595.2	s__Flavobacterium sp000708595	82.1281	904	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCF_003688345.1	s__Flavobacterium sp003688345	82.0635	1009	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018383905.1	s__Flavobacterium branchiicola	82.0065	876	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001686925.1	s__Flavobacterium piscis	81.7886	991	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_004368785.1	s__Flavobacterium sp004368785	81.7024	952	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900129595.1	s__Flavobacterium frigidimaris	81.6892	927	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002217355.1	s__Flavobacterium oncorhynchi	81.6165	834	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	-
GCF_003105115.1	s__Flavobacterium sp003105115	81.5956	860	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804485.1	s__Flavobacterium collinsii	81.286	800	1915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182285.1	s__Flavobacterium sp015182285	81.0728	921	1915	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 13:30:19,451] [INFO] GTDB search result was written to GCF_903819435.1_CIP111411_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:19,452] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:19,456] [INFO] DFAST_QC result json was written to GCF_903819435.1_CIP111411_genomic.fna/dqc_result.json
[2024-01-24 13:30:19,456] [INFO] DFAST_QC completed!
[2024-01-24 13:30:19,456] [INFO] Total running time: 0h2m6s