[2024-01-25 19:06:06,855] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:06,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:06,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg759b8d8f-e51e-4fc8-9c62-5746a2dfd2fe/dqc_reference
[2024-01-25 19:06:08,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:08,011] [INFO] Task started: Prodigal
[2024-01-25 19:06:08,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f5cc8e7-d776-413f-bbb5-97a0ccac5875/GCF_000430025.1_ASM43002v1_genomic.fna.gz | prodigal -d GCF_000430025.1_ASM43002v1_genomic.fna/cds.fna -a GCF_000430025.1_ASM43002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:18,693] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:18,693] [INFO] Task started: HMMsearch
[2024-01-25 19:06:18,693] [INFO] Running command: hmmsearch --tblout GCF_000430025.1_ASM43002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg759b8d8f-e51e-4fc8-9c62-5746a2dfd2fe/dqc_reference/reference_markers.hmm GCF_000430025.1_ASM43002v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:18,950] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:18,952] [INFO] Found 6/6 markers.
[2024-01-25 19:06:18,979] [INFO] Query marker FASTA was written to GCF_000430025.1_ASM43002v1_genomic.fna/markers.fasta
[2024-01-25 19:06:18,980] [INFO] Task started: Blastn
[2024-01-25 19:06:18,980] [INFO] Running command: blastn -query GCF_000430025.1_ASM43002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg759b8d8f-e51e-4fc8-9c62-5746a2dfd2fe/dqc_reference/reference_markers.fasta -out GCF_000430025.1_ASM43002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:19,632] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:19,636] [INFO] Selected 16 target genomes.
[2024-01-25 19:06:19,637] [INFO] Target genome list was writen to GCF_000430025.1_ASM43002v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:19,652] [INFO] Task started: fastANI
[2024-01-25 19:06:19,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5cc8e7-d776-413f-bbb5-97a0ccac5875/GCF_000430025.1_ASM43002v1_genomic.fna.gz --refList GCF_000430025.1_ASM43002v1_genomic.fna/target_genomes.txt --output GCF_000430025.1_ASM43002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:30,269] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:30,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg759b8d8f-e51e-4fc8-9c62-5746a2dfd2fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:30,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg759b8d8f-e51e-4fc8-9c62-5746a2dfd2fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:30,279] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:06:30,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:30,279] [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 suncheonense	strain=DSM 17707	GCA_000430025.1	350894	350894	type	True	100.0	932	932	95	conclusive
Flavobacterium suncheonense	strain=GH29-5	GCA_000769835.1	350894	350894	type	True	99.9845	907	932	95	conclusive
Flavobacterium cauense	strain=R2A-7	GCA_000498475.1	510946	510946	type	True	80.5094	550	932	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000769815.1	510946	510946	type	True	80.4718	559	932	95	below_threshold
Flavobacterium cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	80.4558	553	932	95	below_threshold
Flavobacterium saliperosum	strain=S13	GCA_000498515.1	329186	329186	type	True	80.3797	549	932	95	below_threshold
Flavobacterium saliperosum	strain=CGMCC 1.3801	GCA_900100625.1	329186	329186	type	True	80.3652	558	932	95	below_threshold
Flavobacterium limnosediminis	strain=JC2902	GCA_000498535.1	1401027	1401027	type	True	79.6314	486	932	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000498495.1	1341165	1341165	type	True	79.326	427	932	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000769895.1	1341165	1341165	type	True	79.3239	433	932	95	below_threshold
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	78.2405	287	932	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.84	207	932	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.5481	150	932	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.1088	117	932	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	76.9265	123	932	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	76.6891	140	932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:30,281] [INFO] DFAST Taxonomy check result was written to GCF_000430025.1_ASM43002v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:30,281] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:30,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:30,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg759b8d8f-e51e-4fc8-9c62-5746a2dfd2fe/dqc_reference/checkm_data
[2024-01-25 19:06:30,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:30,311] [INFO] Task started: CheckM
[2024-01-25 19:06:30,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430025.1_ASM43002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430025.1_ASM43002v1_genomic.fna/checkm_input GCF_000430025.1_ASM43002v1_genomic.fna/checkm_result
[2024-01-25 19:07:03,767] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:03,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:03,791] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:03,791] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:03,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430025.1_ASM43002v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:03,791] [INFO] Task started: Blastn
[2024-01-25 19:07:03,792] [INFO] Running command: blastn -query GCF_000430025.1_ASM43002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg759b8d8f-e51e-4fc8-9c62-5746a2dfd2fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430025.1_ASM43002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:04,721] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:04,724] [INFO] Selected 9 target genomes.
[2024-01-25 19:07:04,724] [INFO] Target genome list was writen to GCF_000430025.1_ASM43002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:04,737] [INFO] Task started: fastANI
[2024-01-25 19:07:04,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5cc8e7-d776-413f-bbb5-97a0ccac5875/GCF_000430025.1_ASM43002v1_genomic.fna.gz --refList GCF_000430025.1_ASM43002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430025.1_ASM43002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:10,609] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:10,615] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:10,615] [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_000430025.1	s__Flavobacterium suncheonense	100.0	932	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_000498475.1	s__Flavobacterium cauense	80.4803	553	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900100625.1	s__Flavobacterium saliperosum	80.3652	558	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000498535.1	s__Flavobacterium limnosediminis	79.6421	485	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498495.1	s__Flavobacterium enshiense	79.3139	428	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004801375.1	s__Flavobacterium sp004801375	78.2405	287	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122165.1	s__Flavobacterium sp004122165	77.6522	183	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745595.1	s__Flavobacterium humi	77.4843	201	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525665.1	s__Flavobacterium sp003525665	76.909	113	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:10,617] [INFO] GTDB search result was written to GCF_000430025.1_ASM43002v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:10,617] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:10,622] [INFO] DFAST_QC result json was written to GCF_000430025.1_ASM43002v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:10,622] [INFO] DFAST_QC completed!
[2024-01-25 19:07:10,622] [INFO] Total running time: 0h1m4s