[2024-01-25 18:11:35,648] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,649] [INFO] DQC Reference Directory: /var/lib/cwl/stgef84c7fe-f827-4745-a94c-f1335599e94d/dqc_reference
[2024-01-25 18:11:36,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,780] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,781] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5fff4fd-7465-4a6b-a92e-ba4219e1cf47/GCF_003268855.1_ASM326885v1_genomic.fna.gz | prodigal -d GCF_003268855.1_ASM326885v1_genomic.fna/cds.fna -a GCF_003268855.1_ASM326885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:45,490] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:45,490] [INFO] Task started: HMMsearch
[2024-01-25 18:11:45,490] [INFO] Running command: hmmsearch --tblout GCF_003268855.1_ASM326885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef84c7fe-f827-4745-a94c-f1335599e94d/dqc_reference/reference_markers.hmm GCF_003268855.1_ASM326885v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:45,682] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:45,683] [INFO] Found 6/6 markers.
[2024-01-25 18:11:45,706] [INFO] Query marker FASTA was written to GCF_003268855.1_ASM326885v1_genomic.fna/markers.fasta
[2024-01-25 18:11:45,706] [INFO] Task started: Blastn
[2024-01-25 18:11:45,706] [INFO] Running command: blastn -query GCF_003268855.1_ASM326885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef84c7fe-f827-4745-a94c-f1335599e94d/dqc_reference/reference_markers.fasta -out GCF_003268855.1_ASM326885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:46,332] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:46,335] [INFO] Selected 24 target genomes.
[2024-01-25 18:11:46,335] [INFO] Target genome list was writen to GCF_003268855.1_ASM326885v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:46,371] [INFO] Task started: fastANI
[2024-01-25 18:11:46,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5fff4fd-7465-4a6b-a92e-ba4219e1cf47/GCF_003268855.1_ASM326885v1_genomic.fna.gz --refList GCF_003268855.1_ASM326885v1_genomic.fna/target_genomes.txt --output GCF_003268855.1_ASM326885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:00,874] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:00,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef84c7fe-f827-4745-a94c-f1335599e94d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:00,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef84c7fe-f827-4745-a94c-f1335599e94d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:00,889] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:00,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:00,889] [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 aciduliphilum	strain=DSM 25663	GCA_003268855.1	1101402	1101402	type	True	100.0	897	897	95	conclusive
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	78.7257	258	897	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	78.6671	255	897	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	78.6124	308	897	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	78.6087	310	897	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	78.5725	254	897	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	78.5469	306	897	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	78.1727	254	897	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.951	220	897	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	77.6514	215	897	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	77.6424	175	897	95	below_threshold
Flavobacterium orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	77.4928	171	897	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.3946	199	897	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.3748	133	897	95	below_threshold
Flavobacterium agrisoli	strain=SE-1-e	GCA_016522065.1	2793066	2793066	type	True	77.3397	149	897	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	77.3167	134	897	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.2726	177	897	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	77.2589	149	897	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	77.2563	142	897	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	77.215	126	897	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.0595	148	897	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	76.9957	177	897	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.9726	162	897	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.7418	170	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:00,891] [INFO] DFAST Taxonomy check result was written to GCF_003268855.1_ASM326885v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:00,891] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:00,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:00,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef84c7fe-f827-4745-a94c-f1335599e94d/dqc_reference/checkm_data
[2024-01-25 18:12:00,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:00,922] [INFO] Task started: CheckM
[2024-01-25 18:12:00,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003268855.1_ASM326885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003268855.1_ASM326885v1_genomic.fna/checkm_input GCF_003268855.1_ASM326885v1_genomic.fna/checkm_result
[2024-01-25 18:12:30,778] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:30,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:30,799] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:30,799] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:30,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003268855.1_ASM326885v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:30,800] [INFO] Task started: Blastn
[2024-01-25 18:12:30,800] [INFO] Running command: blastn -query GCF_003268855.1_ASM326885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef84c7fe-f827-4745-a94c-f1335599e94d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003268855.1_ASM326885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:31,691] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:31,699] [INFO] Selected 20 target genomes.
[2024-01-25 18:12:31,700] [INFO] Target genome list was writen to GCF_003268855.1_ASM326885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:31,714] [INFO] Task started: fastANI
[2024-01-25 18:12:31,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5fff4fd-7465-4a6b-a92e-ba4219e1cf47/GCF_003268855.1_ASM326885v1_genomic.fna.gz --refList GCF_003268855.1_ASM326885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003268855.1_ASM326885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:45,223] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:45,236] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:45,236] [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_003268855.1	s__Flavobacterium aciduliphilum	100.0	897	897	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_001464475.1	s__Flavobacterium sp001464475	79.0228	354	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	78.8669	311	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913315.1	s__Flavobacterium sp903913315	78.8242	329	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.66	99.66	0.86	0.86	2	-
GCA_903888655.1	s__Flavobacterium sp903888655	78.6967	260	897	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	78.6087	310	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_012911605.1	s__Flavobacterium sp012911605	78.5725	254	897	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	78.4193	269	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303755.1	s__Flavobacterium sp017303755	78.4048	278	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787805.1	s__Flavobacterium sp016787805	78.3084	284	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838055.1	s__Flavobacterium sp903838055	78.274	310	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.95	0.98	0.97	3	-
GCF_004362665.1	s__Flavobacterium dankookense	78.2051	253	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169355.1	s__Flavobacterium sp000169355	77.6544	207	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_009707955.1	s__Flavobacterium sp009707955	77.4617	143	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000708595.2	s__Flavobacterium sp000708595	77.3346	144	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCF_004349085.1	s__Flavobacterium caseinilyticum	77.1951	126	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822155.1	s__Flavobacterium sp013822155	77.1827	166	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752255.1	s__Flavobacterium sp015752255	77.1529	155	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984835.1	s__Flavobacterium sp017984835	77.0551	184	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.46	99.46	0.94	0.94	2	-
GCF_013294005.1	s__Flavobacterium sp013294005	76.9313	146	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.41	97.36	0.86	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:45,237] [INFO] GTDB search result was written to GCF_003268855.1_ASM326885v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:45,238] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:45,242] [INFO] DFAST_QC result json was written to GCF_003268855.1_ASM326885v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:45,242] [INFO] DFAST_QC completed!
[2024-01-25 18:12:45,242] [INFO] Total running time: 0h1m10s