[2024-01-24 15:01:23,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:23,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:23,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg950cda03-80aa-449c-a5ff-30f122ac0141/dqc_reference
[2024-01-24 15:01:24,565] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:24,566] [INFO] Task started: Prodigal
[2024-01-24 15:01:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg02634324-e1cd-4c8a-a731-0b96dc99e6b9/GCF_004345565.1_ASM434556v1_genomic.fna.gz | prodigal -d GCF_004345565.1_ASM434556v1_genomic.fna/cds.fna -a GCF_004345565.1_ASM434556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:46,078] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:46,079] [INFO] Task started: HMMsearch
[2024-01-24 15:01:46,079] [INFO] Running command: hmmsearch --tblout GCF_004345565.1_ASM434556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg950cda03-80aa-449c-a5ff-30f122ac0141/dqc_reference/reference_markers.hmm GCF_004345565.1_ASM434556v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:46,482] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:46,484] [INFO] Found 6/6 markers.
[2024-01-24 15:01:46,536] [INFO] Query marker FASTA was written to GCF_004345565.1_ASM434556v1_genomic.fna/markers.fasta
[2024-01-24 15:01:46,536] [INFO] Task started: Blastn
[2024-01-24 15:01:46,537] [INFO] Running command: blastn -query GCF_004345565.1_ASM434556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg950cda03-80aa-449c-a5ff-30f122ac0141/dqc_reference/reference_markers.fasta -out GCF_004345565.1_ASM434556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:47,307] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:47,311] [INFO] Selected 20 target genomes.
[2024-01-24 15:01:47,312] [INFO] Target genome list was writen to GCF_004345565.1_ASM434556v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:47,338] [INFO] Task started: fastANI
[2024-01-24 15:01:47,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg02634324-e1cd-4c8a-a731-0b96dc99e6b9/GCF_004345565.1_ASM434556v1_genomic.fna.gz --refList GCF_004345565.1_ASM434556v1_genomic.fna/target_genomes.txt --output GCF_004345565.1_ASM434556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:11,749] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:11,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg950cda03-80aa-449c-a5ff-30f122ac0141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:11,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg950cda03-80aa-449c-a5ff-30f122ac0141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:11,771] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:11,771] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:11,771] [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 circumlabens	strain=P5626	GCA_004345565.1	2133765	2133765	type	True	100.0	1900	1900	95	conclusive
Flavobacterium circumlabens	strain=CCM 8828	GCA_004369705.1	2133765	2133765	type	True	99.9988	1897	1900	95	conclusive
Flavobacterium cupreum	strain=CCM 8825	GCA_003996965.1	2133766	2133766	type	True	89.8877	1482	1900	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	82.9665	1126	1900	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.9035	1136	1900	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	82.7417	1047	1900	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	82.7286	1051	1900	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	82.7114	1056	1900	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	82.709	1028	1900	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	82.6256	1019	1900	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	82.2751	938	1900	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	82.2164	935	1900	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.8393	992	1900	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	81.8091	939	1900	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	81.7971	1045	1900	95	below_threshold
Flavobacterium cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	81.2009	831	1900	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	80.8484	944	1900	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	80.7969	901	1900	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	80.6827	931	1900	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.6752	129	1900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:11,773] [INFO] DFAST Taxonomy check result was written to GCF_004345565.1_ASM434556v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:11,774] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:11,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:11,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg950cda03-80aa-449c-a5ff-30f122ac0141/dqc_reference/checkm_data
[2024-01-24 15:02:11,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:11,835] [INFO] Task started: CheckM
[2024-01-24 15:02:11,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004345565.1_ASM434556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004345565.1_ASM434556v1_genomic.fna/checkm_input GCF_004345565.1_ASM434556v1_genomic.fna/checkm_result
[2024-01-24 15:03:12,904] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:12,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:12,929] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:12,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:12,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004345565.1_ASM434556v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:12,931] [INFO] Task started: Blastn
[2024-01-24 15:03:12,931] [INFO] Running command: blastn -query GCF_004345565.1_ASM434556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg950cda03-80aa-449c-a5ff-30f122ac0141/dqc_reference/reference_markers_gtdb.fasta -out GCF_004345565.1_ASM434556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:14,046] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:14,050] [INFO] Selected 17 target genomes.
[2024-01-24 15:03:14,050] [INFO] Target genome list was writen to GCF_004345565.1_ASM434556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:14,108] [INFO] Task started: fastANI
[2024-01-24 15:03:14,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg02634324-e1cd-4c8a-a731-0b96dc99e6b9/GCF_004345565.1_ASM434556v1_genomic.fna.gz --refList GCF_004345565.1_ASM434556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004345565.1_ASM434556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:37,350] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:37,374] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:37,374] [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_004345565.1	s__Flavobacterium circumlabens	100.0	1900	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.60	96.60	0.85	0.85	2	conclusive
GCF_009674775.1	s__Flavobacterium sp009674775	89.9183	1449	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003996965.1	s__Flavobacterium cupreum	89.8799	1483	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688345.1	s__Flavobacterium sp003688345	83.0644	1116	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003105115.1	s__Flavobacterium sp003105115	82.9761	1057	1900	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	82.8822	1102	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011751075.1	s__Flavobacterium sp011751075	82.8212	1025	1900	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	82.7038	1057	1900	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	82.6944	1062	1900	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	82.6592	1026	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_900107365.1	s__Flavobacterium aquidurense	82.6243	1014	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014844035.1	s__Flavobacterium sp014844035	82.61	1098	1900	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	82.5891	1080	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	82.5622	1143	1900	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	82.2479	1100	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789235.1	s__Flavobacterium sp009789235	81.8195	938	1900	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	81.7241	968	1900	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 15:03:37,379] [INFO] GTDB search result was written to GCF_004345565.1_ASM434556v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:37,380] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:37,387] [INFO] DFAST_QC result json was written to GCF_004345565.1_ASM434556v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:37,387] [INFO] DFAST_QC completed!
[2024-01-24 15:03:37,388] [INFO] Total running time: 0h2m14s