[2024-01-24 11:20:04,203] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,205] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg54fb9016-3e69-4108-8425-7436796c5d3d/dqc_reference
[2024-01-24 11:20:05,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,358] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg19e30b09-9fc0-484d-8f7f-84c41b446a57/GCF_004797125.1_ASM479712v1_genomic.fna.gz | prodigal -d GCF_004797125.1_ASM479712v1_genomic.fna/cds.fna -a GCF_004797125.1_ASM479712v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:17,792] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:17,792] [INFO] Task started: HMMsearch
[2024-01-24 11:20:17,792] [INFO] Running command: hmmsearch --tblout GCF_004797125.1_ASM479712v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54fb9016-3e69-4108-8425-7436796c5d3d/dqc_reference/reference_markers.hmm GCF_004797125.1_ASM479712v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:17,982] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:17,983] [INFO] Found 6/6 markers.
[2024-01-24 11:20:18,008] [INFO] Query marker FASTA was written to GCF_004797125.1_ASM479712v1_genomic.fna/markers.fasta
[2024-01-24 11:20:18,008] [INFO] Task started: Blastn
[2024-01-24 11:20:18,008] [INFO] Running command: blastn -query GCF_004797125.1_ASM479712v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54fb9016-3e69-4108-8425-7436796c5d3d/dqc_reference/reference_markers.fasta -out GCF_004797125.1_ASM479712v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:18,673] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:18,676] [INFO] Selected 17 target genomes.
[2024-01-24 11:20:18,677] [INFO] Target genome list was writen to GCF_004797125.1_ASM479712v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:18,683] [INFO] Task started: fastANI
[2024-01-24 11:20:18,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e30b09-9fc0-484d-8f7f-84c41b446a57/GCF_004797125.1_ASM479712v1_genomic.fna.gz --refList GCF_004797125.1_ASM479712v1_genomic.fna/target_genomes.txt --output GCF_004797125.1_ASM479712v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:28,243] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:28,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54fb9016-3e69-4108-8425-7436796c5d3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:28,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54fb9016-3e69-4108-8425-7436796c5d3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:28,257] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:28,257] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:28,257] [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 sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	100.0	1042	1043	95	conclusive
Flavobacterium phycosphaerae	strain=MK012	GCA_010119235.1	2697515	2697515	type	True	79.8177	520	1043	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	79.3799	437	1043	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	79.3279	439	1043	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	79.2259	425	1043	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	79.2071	431	1043	95	below_threshold
Flavobacterium silvisoli	strain=RD-2-33	GCA_004329815.1	2529433	2529433	type	True	79.0526	418	1043	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	78.5339	383	1043	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	78.4637	378	1043	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	78.4195	376	1043	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	78.3788	243	1043	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.0298	232	1043	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.8155	240	1043	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.7792	247	1043	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	77.5835	211	1043	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.5135	165	1043	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.472	182	1043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:28,259] [INFO] DFAST Taxonomy check result was written to GCF_004797125.1_ASM479712v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:28,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:28,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:28,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54fb9016-3e69-4108-8425-7436796c5d3d/dqc_reference/checkm_data
[2024-01-24 11:20:28,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:28,291] [INFO] Task started: CheckM
[2024-01-24 11:20:28,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004797125.1_ASM479712v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004797125.1_ASM479712v1_genomic.fna/checkm_input GCF_004797125.1_ASM479712v1_genomic.fna/checkm_result
[2024-01-24 11:21:06,803] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:06,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:06,819] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:06,819] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:06,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004797125.1_ASM479712v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:06,819] [INFO] Task started: Blastn
[2024-01-24 11:21:06,819] [INFO] Running command: blastn -query GCF_004797125.1_ASM479712v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54fb9016-3e69-4108-8425-7436796c5d3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004797125.1_ASM479712v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:07,760] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:07,763] [INFO] Selected 13 target genomes.
[2024-01-24 11:21:07,763] [INFO] Target genome list was writen to GCF_004797125.1_ASM479712v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:07,772] [INFO] Task started: fastANI
[2024-01-24 11:21:07,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e30b09-9fc0-484d-8f7f-84c41b446a57/GCF_004797125.1_ASM479712v1_genomic.fna.gz --refList GCF_004797125.1_ASM479712v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004797125.1_ASM479712v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:17,061] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:17,072] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:17,072] [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_004797125.1	s__Flavobacterium sangjuense	100.0	1042	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002296885.1	s__Flavobacterium sp002296885	80.8784	448	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634615.1	s__Flavobacterium sp002482945	80.3155	578	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
GCF_014486695.1	s__Flavobacterium buctense	80.0485	499	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742145.1	s__Flavobacterium sp011742145	79.9018	526	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010119235.1	s__Flavobacterium phycosphaerae	79.854	520	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013072765.1	s__Flavobacterium sp013072765	79.6038	522	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911605.1	s__Flavobacterium sp012911605	79.3893	436	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	79.3327	438	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486675.1	s__Flavobacterium macrobrachii	79.2116	430	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCA_003525665.1	s__Flavobacterium sp003525665	78.6377	343	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	78.5339	383	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_001857965.1	s__Flavobacterium commune	78.3229	241	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:17,075] [INFO] GTDB search result was written to GCF_004797125.1_ASM479712v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:17,075] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:17,079] [INFO] DFAST_QC result json was written to GCF_004797125.1_ASM479712v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:17,079] [INFO] DFAST_QC completed!
[2024-01-24 11:21:17,079] [INFO] Total running time: 0h1m13s