[2024-01-24 13:57:13,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d198cc0-ac37-42f2-8c2e-0187afc4d868/dqc_reference
[2024-01-24 13:57:14,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,857] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,858] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdd34d65-2f26-4a34-a3a9-74689231f3a8/GCF_003202435.1_ASM320243v1_genomic.fna.gz | prodigal -d GCF_003202435.1_ASM320243v1_genomic.fna/cds.fna -a GCF_003202435.1_ASM320243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:32,400] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:32,400] [INFO] Task started: HMMsearch
[2024-01-24 13:57:32,400] [INFO] Running command: hmmsearch --tblout GCF_003202435.1_ASM320243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d198cc0-ac37-42f2-8c2e-0187afc4d868/dqc_reference/reference_markers.hmm GCF_003202435.1_ASM320243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:32,697] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:32,698] [INFO] Found 6/6 markers.
[2024-01-24 13:57:32,741] [INFO] Query marker FASTA was written to GCF_003202435.1_ASM320243v1_genomic.fna/markers.fasta
[2024-01-24 13:57:32,741] [INFO] Task started: Blastn
[2024-01-24 13:57:32,741] [INFO] Running command: blastn -query GCF_003202435.1_ASM320243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d198cc0-ac37-42f2-8c2e-0187afc4d868/dqc_reference/reference_markers.fasta -out GCF_003202435.1_ASM320243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:33,436] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:33,439] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:33,440] [INFO] Target genome list was writen to GCF_003202435.1_ASM320243v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:33,443] [INFO] Task started: fastANI
[2024-01-24 13:57:33,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdd34d65-2f26-4a34-a3a9-74689231f3a8/GCF_003202435.1_ASM320243v1_genomic.fna.gz --refList GCF_003202435.1_ASM320243v1_genomic.fna/target_genomes.txt --output GCF_003202435.1_ASM320243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:52,470] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:52,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d198cc0-ac37-42f2-8c2e-0187afc4d868/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:52,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d198cc0-ac37-42f2-8c2e-0187afc4d868/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:52,485] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:52,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:52,486] [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 cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	100.0	1710	1713	95	conclusive
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	86.0318	1201	1713	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	85.9342	1209	1713	95	below_threshold
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	84.6417	1153	1713	95	below_threshold
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	84.5979	1178	1713	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	84.3234	1105	1713	95	below_threshold
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	84.0492	1011	1713	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.5288	871	1713	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	81.2287	813	1713	95	below_threshold
Flavobacterium cupreum	strain=CCM 8825	GCA_003996965.1	2133766	2133766	type	True	81.2251	798	1713	95	below_threshold
Flavobacterium collinsii		GCA_902804485.1	1114861	1114861	type	True	81.2057	757	1713	95	below_threshold
Flavobacterium circumlabens	strain=P5626	GCA_004345565.1	2133765	2133765	type	True	81.0814	850	1713	95	below_threshold
Flavobacterium circumlabens	strain=CCM 8828	GCA_004369705.1	2133765	2133765	type	True	81.0303	846	1713	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	80.9825	833	1713	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	80.839	799	1713	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	80.7259	859	1713	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.2375	168	1713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:52,488] [INFO] DFAST Taxonomy check result was written to GCF_003202435.1_ASM320243v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:52,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:52,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:52,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d198cc0-ac37-42f2-8c2e-0187afc4d868/dqc_reference/checkm_data
[2024-01-24 13:57:52,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:52,554] [INFO] Task started: CheckM
[2024-01-24 13:57:52,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003202435.1_ASM320243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003202435.1_ASM320243v1_genomic.fna/checkm_input GCF_003202435.1_ASM320243v1_genomic.fna/checkm_result
[2024-01-24 13:58:48,132] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:48,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:48,152] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:48,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:48,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003202435.1_ASM320243v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:48,153] [INFO] Task started: Blastn
[2024-01-24 13:58:48,154] [INFO] Running command: blastn -query GCF_003202435.1_ASM320243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d198cc0-ac37-42f2-8c2e-0187afc4d868/dqc_reference/reference_markers_gtdb.fasta -out GCF_003202435.1_ASM320243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:49,161] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:49,165] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:49,165] [INFO] Target genome list was writen to GCF_003202435.1_ASM320243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:49,179] [INFO] Task started: fastANI
[2024-01-24 13:58:49,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdd34d65-2f26-4a34-a3a9-74689231f3a8/GCF_003202435.1_ASM320243v1_genomic.fna.gz --refList GCF_003202435.1_ASM320243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003202435.1_ASM320243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:07,187] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:07,206] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:07,207] [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_003202435.1	s__Flavobacterium cheongpyeongense	100.0	1710	1713	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_003202405.1	s__Flavobacterium hydrophilum	85.9242	1211	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735715.2	s__Flavobacterium chungangense	85.6138	1178	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_010645075.1	s__Flavobacterium limi	84.5962	1178	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010645065.1	s__Flavobacterium fluviatile	84.0564	1010	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614725.1	s__Flavobacterium ajazii	83.4297	1136	1713	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	83.2942	1062	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003105115.1	s__Flavobacterium sp003105115	81.7473	820	1713	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	81.6895	874	1713	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	81.5839	871	1713	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	81.5345	815	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018383905.1	s__Flavobacterium branchiicola	81.5079	839	1713	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	81.4856	914	1713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCF_009711165.2	s__Flavobacterium sp009711165	81.0675	888	1713	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 13:59:07,208] [INFO] GTDB search result was written to GCF_003202435.1_ASM320243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:07,209] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:07,213] [INFO] DFAST_QC result json was written to GCF_003202435.1_ASM320243v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:07,214] [INFO] DFAST_QC completed!
[2024-01-24 13:59:07,214] [INFO] Total running time: 0h1m54s