[2024-01-24 14:38:47,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:47,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:47,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg341bc074-183f-43c8-9a68-b7d01261f9b1/dqc_reference
[2024-01-24 14:38:50,444] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,446] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,447] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcb6065f-006c-458e-91d5-66d862831286/GCF_003996965.1_ASM399696v1_genomic.fna.gz | prodigal -d GCF_003996965.1_ASM399696v1_genomic.fna/cds.fna -a GCF_003996965.1_ASM399696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:13,344] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:13,344] [INFO] Task started: HMMsearch
[2024-01-24 14:39:13,344] [INFO] Running command: hmmsearch --tblout GCF_003996965.1_ASM399696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg341bc074-183f-43c8-9a68-b7d01261f9b1/dqc_reference/reference_markers.hmm GCF_003996965.1_ASM399696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:13,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:13,764] [INFO] Found 6/6 markers.
[2024-01-24 14:39:13,837] [INFO] Query marker FASTA was written to GCF_003996965.1_ASM399696v1_genomic.fna/markers.fasta
[2024-01-24 14:39:13,837] [INFO] Task started: Blastn
[2024-01-24 14:39:13,837] [INFO] Running command: blastn -query GCF_003996965.1_ASM399696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg341bc074-183f-43c8-9a68-b7d01261f9b1/dqc_reference/reference_markers.fasta -out GCF_003996965.1_ASM399696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:14,628] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:14,632] [INFO] Selected 18 target genomes.
[2024-01-24 14:39:14,633] [INFO] Target genome list was writen to GCF_003996965.1_ASM399696v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:14,646] [INFO] Task started: fastANI
[2024-01-24 14:39:14,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcb6065f-006c-458e-91d5-66d862831286/GCF_003996965.1_ASM399696v1_genomic.fna.gz --refList GCF_003996965.1_ASM399696v1_genomic.fna/target_genomes.txt --output GCF_003996965.1_ASM399696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:39,211] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:39,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg341bc074-183f-43c8-9a68-b7d01261f9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:39,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg341bc074-183f-43c8-9a68-b7d01261f9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:39,227] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:39,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:39,228] [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 cupreum	strain=CCM 8825	GCA_003996965.1	2133766	2133766	type	True	100.0	1924	1925	95	conclusive
Flavobacterium circumlabens	strain=CCM 8828	GCA_004369705.1	2133765	2133765	type	True	89.8571	1477	1925	95	below_threshold
Flavobacterium circumlabens	strain=P5626	GCA_004345565.1	2133765	2133765	type	True	89.7802	1473	1925	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	82.5645	1002	1925	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	82.5306	1027	1925	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	82.3671	1055	1925	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	82.2368	1003	1925	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	81.7882	938	1925	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	81.7846	947	1925	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	81.5756	905	1925	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	81.5088	999	1925	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	81.4961	870	1925	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.3467	968	1925	95	below_threshold
Flavobacterium cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	81.1744	802	1925	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	80.5428	926	1925	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	80.5079	887	1925	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	80.4284	870	1925	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.4046	175	1925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:39,229] [INFO] DFAST Taxonomy check result was written to GCF_003996965.1_ASM399696v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:39,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:39,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:39,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg341bc074-183f-43c8-9a68-b7d01261f9b1/dqc_reference/checkm_data
[2024-01-24 14:39:39,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:39,292] [INFO] Task started: CheckM
[2024-01-24 14:39:39,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003996965.1_ASM399696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003996965.1_ASM399696v1_genomic.fna/checkm_input GCF_003996965.1_ASM399696v1_genomic.fna/checkm_result
[2024-01-24 14:40:43,613] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:43,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:43,636] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:43,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:43,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003996965.1_ASM399696v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:43,638] [INFO] Task started: Blastn
[2024-01-24 14:40:43,638] [INFO] Running command: blastn -query GCF_003996965.1_ASM399696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg341bc074-183f-43c8-9a68-b7d01261f9b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003996965.1_ASM399696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:44,624] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:44,629] [INFO] Selected 15 target genomes.
[2024-01-24 14:40:44,629] [INFO] Target genome list was writen to GCF_003996965.1_ASM399696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:44,641] [INFO] Task started: fastANI
[2024-01-24 14:40:44,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcb6065f-006c-458e-91d5-66d862831286/GCF_003996965.1_ASM399696v1_genomic.fna.gz --refList GCF_003996965.1_ASM399696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003996965.1_ASM399696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:04,701] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:04,715] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:04,715] [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_003996965.1	s__Flavobacterium cupreum	100.0	1924	1925	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_009674775.1	s__Flavobacterium sp009674775	90.5452	1402	1925	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	89.794	1472	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.60	96.60	0.85	0.85	2	-
GCF_001686925.1	s__Flavobacterium piscis	82.5324	1026	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_001404985.1	s__Flavobacterium aquidurense_B	82.5126	1014	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975985.1	s__Flavobacterium sp001975985	82.3678	1047	1925	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	82.3557	1035	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011751075.1	s__Flavobacterium sp011751075	82.3355	1000	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014844035.1	s__Flavobacterium sp014844035	82.2942	1053	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217415.1	s__Flavobacterium sp003217415	82.2593	1016	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
GCA_900107365.1	s__Flavobacterium aquidurense	82.2536	1006	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900142735.1	s__Flavobacterium saccharophilum	82.2424	1002	1925	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422725.1	s__Flavobacterium sp001422725	82.1809	1065	1925	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	81.8258	1053	1925	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	81.4416	935	1925	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 14:41:04,717] [INFO] GTDB search result was written to GCF_003996965.1_ASM399696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:04,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:04,722] [INFO] DFAST_QC result json was written to GCF_003996965.1_ASM399696v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:04,722] [INFO] DFAST_QC completed!
[2024-01-24 14:41:04,722] [INFO] Total running time: 0h2m17s