[2024-01-24 13:13:26,451] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:26,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:26,458] [INFO] DQC Reference Directory: /var/lib/cwl/stge20bf5e2-5246-402e-8c95-50693740bf2b/dqc_reference
[2024-01-24 13:13:27,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:27,780] [INFO] Task started: Prodigal
[2024-01-24 13:13:27,780] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdfc97aa-2587-4ef9-bc5e-118afc2e9208/GCF_002217285.1_ASM221728v1_genomic.fna.gz | prodigal -d GCF_002217285.1_ASM221728v1_genomic.fna/cds.fna -a GCF_002217285.1_ASM221728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:46,058] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:46,058] [INFO] Task started: HMMsearch
[2024-01-24 13:13:46,058] [INFO] Running command: hmmsearch --tblout GCF_002217285.1_ASM221728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge20bf5e2-5246-402e-8c95-50693740bf2b/dqc_reference/reference_markers.hmm GCF_002217285.1_ASM221728v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:46,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:46,401] [INFO] Found 6/6 markers.
[2024-01-24 13:13:46,454] [INFO] Query marker FASTA was written to GCF_002217285.1_ASM221728v1_genomic.fna/markers.fasta
[2024-01-24 13:13:46,455] [INFO] Task started: Blastn
[2024-01-24 13:13:46,455] [INFO] Running command: blastn -query GCF_002217285.1_ASM221728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge20bf5e2-5246-402e-8c95-50693740bf2b/dqc_reference/reference_markers.fasta -out GCF_002217285.1_ASM221728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:47,156] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:47,159] [INFO] Selected 21 target genomes.
[2024-01-24 13:13:47,160] [INFO] Target genome list was writen to GCF_002217285.1_ASM221728v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:47,169] [INFO] Task started: fastANI
[2024-01-24 13:13:47,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdfc97aa-2587-4ef9-bc5e-118afc2e9208/GCF_002217285.1_ASM221728v1_genomic.fna.gz --refList GCF_002217285.1_ASM221728v1_genomic.fna/target_genomes.txt --output GCF_002217285.1_ASM221728v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:09,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:09,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge20bf5e2-5246-402e-8c95-50693740bf2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:09,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge20bf5e2-5246-402e-8c95-50693740bf2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:09,929] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:09,929] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:09,930] [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 hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	100.0	1699	1708	95	conclusive
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	82.7317	933	1708	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	82.6999	966	1708	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	82.5829	1018	1708	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	82.5754	984	1708	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	82.4957	972	1708	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.4771	1030	1708	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	82.4105	963	1708	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	82.3881	901	1708	95	below_threshold
Flavobacterium hibernum	strain=DSM 12611	GCA_000832125.1	37752	37752	type	True	82.3214	917	1708	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	82.2783	928	1708	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	82.2671	971	1708	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	82.2657	904	1708	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.8355	887	1708	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	81.7211	818	1708	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	81.5071	915	1708	95	below_threshold
Flavobacterium cupreum	strain=CCM 8825	GCA_003996965.1	2133766	2133766	type	True	81.4589	887	1708	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.0551	885	1708	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.0359	878	1708	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.0083	853	1708	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.9003	158	1708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,931] [INFO] DFAST Taxonomy check result was written to GCF_002217285.1_ASM221728v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:09,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:09,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:09,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge20bf5e2-5246-402e-8c95-50693740bf2b/dqc_reference/checkm_data
[2024-01-24 13:14:09,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:09,989] [INFO] Task started: CheckM
[2024-01-24 13:14:09,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217285.1_ASM221728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217285.1_ASM221728v1_genomic.fna/checkm_input GCF_002217285.1_ASM221728v1_genomic.fna/checkm_result
[2024-01-24 13:15:01,998] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:01,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:02,017] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:02,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:02,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217285.1_ASM221728v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:02,018] [INFO] Task started: Blastn
[2024-01-24 13:15:02,019] [INFO] Running command: blastn -query GCF_002217285.1_ASM221728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge20bf5e2-5246-402e-8c95-50693740bf2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217285.1_ASM221728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:03,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:03,113] [INFO] Selected 22 target genomes.
[2024-01-24 13:15:03,114] [INFO] Target genome list was writen to GCF_002217285.1_ASM221728v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:03,147] [INFO] Task started: fastANI
[2024-01-24 13:15:03,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdfc97aa-2587-4ef9-bc5e-118afc2e9208/GCF_002217285.1_ASM221728v1_genomic.fna.gz --refList GCF_002217285.1_ASM221728v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217285.1_ASM221728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:28,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:28,763] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:28,764] [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_002217285.1	s__Flavobacterium hercynium	100.0	1699	1708	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_009707955.1	s__Flavobacterium sp009707955	82.9079	1024	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004362015.1	s__Flavobacterium sp004362015	82.8086	966	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804475.1	s__Flavobacterium bizetiae	82.7495	931	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCA_001507425.1	s__Flavobacterium sp001507425	82.728	1015	1708	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	82.7229	1013	1708	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	82.6759	1013	1708	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	82.5873	969	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018380615.1	s__Flavobacterium psychroterrae	82.5685	984	1708	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	82.5441	980	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.90	98.90	0.89	0.89	2	-
GCF_001686925.1	s__Flavobacterium piscis	82.4796	974	1708	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	82.4724	1002	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339525.1	s__Flavobacterium sp004339525	82.4681	985	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900142715.1	s__Flavobacterium pectinovorum	82.4605	1031	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.60	0.94	0.89	3	-
GCF_003217415.1	s__Flavobacterium sp003217415	82.4072	979	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
GCF_000832125.1	s__Flavobacterium hibernum	82.3136	918	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_002222055.1	s__Flavobacterium araucananum	82.2981	967	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	82.2726	982	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142735.1	s__Flavobacterium saccharophilum	82.2568	906	1708	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	81.7156	819	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
GCF_009674775.1	s__Flavobacterium sp009674775	81.6604	863	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217435.1	s__Flavobacterium reichenbachii	81.4997	916	1708	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:28,766] [INFO] GTDB search result was written to GCF_002217285.1_ASM221728v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:28,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:28,771] [INFO] DFAST_QC result json was written to GCF_002217285.1_ASM221728v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:28,771] [INFO] DFAST_QC completed!
[2024-01-24 13:15:28,771] [INFO] Total running time: 0h2m2s