[2024-01-24 12:06:24,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,170] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,171] [INFO] DQC Reference Directory: /var/lib/cwl/stga9fc8f7e-1e4c-42c4-86ee-2bda6c099946/dqc_reference
[2024-01-24 12:06:25,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,531] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg21dd0ea4-5064-465a-a7d4-7df06485decd/GCF_003097655.1_ASM309765v1_genomic.fna.gz | prodigal -d GCF_003097655.1_ASM309765v1_genomic.fna/cds.fna -a GCF_003097655.1_ASM309765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:41,645] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:41,646] [INFO] Task started: HMMsearch
[2024-01-24 12:06:41,646] [INFO] Running command: hmmsearch --tblout GCF_003097655.1_ASM309765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9fc8f7e-1e4c-42c4-86ee-2bda6c099946/dqc_reference/reference_markers.hmm GCF_003097655.1_ASM309765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:41,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:41,897] [INFO] Found 6/6 markers.
[2024-01-24 12:06:41,929] [INFO] Query marker FASTA was written to GCF_003097655.1_ASM309765v1_genomic.fna/markers.fasta
[2024-01-24 12:06:41,930] [INFO] Task started: Blastn
[2024-01-24 12:06:41,930] [INFO] Running command: blastn -query GCF_003097655.1_ASM309765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9fc8f7e-1e4c-42c4-86ee-2bda6c099946/dqc_reference/reference_markers.fasta -out GCF_003097655.1_ASM309765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:42,617] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:42,620] [INFO] Selected 23 target genomes.
[2024-01-24 12:06:42,621] [INFO] Target genome list was writen to GCF_003097655.1_ASM309765v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:42,641] [INFO] Task started: fastANI
[2024-01-24 12:06:42,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg21dd0ea4-5064-465a-a7d4-7df06485decd/GCF_003097655.1_ASM309765v1_genomic.fna.gz --refList GCF_003097655.1_ASM309765v1_genomic.fna/target_genomes.txt --output GCF_003097655.1_ASM309765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:00,004] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:00,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9fc8f7e-1e4c-42c4-86ee-2bda6c099946/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:00,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9fc8f7e-1e4c-42c4-86ee-2bda6c099946/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:00,022] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:00,022] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:00,022] [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 laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	100.0	1287	1289	95	conclusive
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	83.0368	838	1289	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	82.6951	814	1289	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_000735535.1	1492737	1492737	type	True	80.4096	614	1289	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	80.4076	669	1289	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_001761465.1	1492737	1492737	type	True	80.3707	659	1289	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	80.0341	548	1289	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	79.982	534	1289	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.9373	525	1289	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	79.7304	536	1289	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	79.7067	493	1289	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	79.6542	437	1289	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.5559	496	1289	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.1334	410	1289	95	below_threshold
Flavobacterium frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	78.9941	426	1289	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	78.9685	431	1289	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	78.829	441	1289	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	78.8023	345	1289	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	78.75	381	1289	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.3021	369	1289	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.1219	365	1289	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	76.8763	159	1289	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.8918	72	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:00,025] [INFO] DFAST Taxonomy check result was written to GCF_003097655.1_ASM309765v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:00,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:00,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:00,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9fc8f7e-1e4c-42c4-86ee-2bda6c099946/dqc_reference/checkm_data
[2024-01-24 12:07:00,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:00,065] [INFO] Task started: CheckM
[2024-01-24 12:07:00,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003097655.1_ASM309765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003097655.1_ASM309765v1_genomic.fna/checkm_input GCF_003097655.1_ASM309765v1_genomic.fna/checkm_result
[2024-01-24 12:07:44,400] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:44,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:44,425] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:44,425] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:44,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003097655.1_ASM309765v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:44,426] [INFO] Task started: Blastn
[2024-01-24 12:07:44,426] [INFO] Running command: blastn -query GCF_003097655.1_ASM309765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9fc8f7e-1e4c-42c4-86ee-2bda6c099946/dqc_reference/reference_markers_gtdb.fasta -out GCF_003097655.1_ASM309765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:45,347] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:45,350] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:45,351] [INFO] Target genome list was writen to GCF_003097655.1_ASM309765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:45,379] [INFO] Task started: fastANI
[2024-01-24 12:07:45,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg21dd0ea4-5064-465a-a7d4-7df06485decd/GCF_003097655.1_ASM309765v1_genomic.fna.gz --refList GCF_003097655.1_ASM309765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003097655.1_ASM309765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:58,015] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:58,028] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:58,028] [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_003097655.1	s__Flavobacterium laiguense	100.0	1287	1289	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_007097385.1	s__Flavobacterium sp007097385	88.6607	1009	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284035.1	s__Flavobacterium sp003096795	82.9474	829	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCF_003254745.1	s__Flavobacterium aquariorum	82.6901	815	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001005.1	s__Flavobacterium sp002001005	82.5785	779	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797935.1	s__Flavobacterium sp002797935	81.4852	724	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813295.1	s__Flavobacterium sp002813295	81.0422	713	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761465.1	s__Flavobacterium gilvum	80.3734	658	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004349195.1	s__Flavobacterium sp004349195	80.0184	550	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812945.1	s__Flavobacterium sp000812945	80.0157	536	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097265.1	s__Flavobacterium gawalongense	79.9512	523	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_000744835.1	s__Flavobacterium sp000744835	79.7832	498	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	79.1609	407	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294005.1	s__Flavobacterium sp013294005	79.0538	376	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.41	97.36	0.86	0.85	3	-
GCF_007097365.1	s__Flavobacterium franklandianum	78.8301	442	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:58,030] [INFO] GTDB search result was written to GCF_003097655.1_ASM309765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:58,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:58,035] [INFO] DFAST_QC result json was written to GCF_003097655.1_ASM309765v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:58,035] [INFO] DFAST_QC completed!
[2024-01-24 12:07:58,035] [INFO] Total running time: 0h1m34s