[2024-01-24 14:14:04,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:04,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:04,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg703a2cd6-6503-4662-bc25-5c7c28727722/dqc_reference
[2024-01-24 14:14:06,310] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:06,311] [INFO] Task started: Prodigal
[2024-01-24 14:14:06,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a0c7a71-1864-43e9-9108-fcf299d149b8/GCF_027474525.2_ASM2747452v2_genomic.fna.gz | prodigal -d GCF_027474525.2_ASM2747452v2_genomic.fna/cds.fna -a GCF_027474525.2_ASM2747452v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:20,393] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:20,393] [INFO] Task started: HMMsearch
[2024-01-24 14:14:20,394] [INFO] Running command: hmmsearch --tblout GCF_027474525.2_ASM2747452v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg703a2cd6-6503-4662-bc25-5c7c28727722/dqc_reference/reference_markers.hmm GCF_027474525.2_ASM2747452v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:20,667] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:20,669] [INFO] Found 6/6 markers.
[2024-01-24 14:14:20,700] [INFO] Query marker FASTA was written to GCF_027474525.2_ASM2747452v2_genomic.fna/markers.fasta
[2024-01-24 14:14:20,701] [INFO] Task started: Blastn
[2024-01-24 14:14:20,701] [INFO] Running command: blastn -query GCF_027474525.2_ASM2747452v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg703a2cd6-6503-4662-bc25-5c7c28727722/dqc_reference/reference_markers.fasta -out GCF_027474525.2_ASM2747452v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:21,430] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:21,434] [INFO] Selected 20 target genomes.
[2024-01-24 14:14:21,434] [INFO] Target genome list was writen to GCF_027474525.2_ASM2747452v2_genomic.fna/target_genomes.txt
[2024-01-24 14:14:21,450] [INFO] Task started: fastANI
[2024-01-24 14:14:21,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a0c7a71-1864-43e9-9108-fcf299d149b8/GCF_027474525.2_ASM2747452v2_genomic.fna.gz --refList GCF_027474525.2_ASM2747452v2_genomic.fna/target_genomes.txt --output GCF_027474525.2_ASM2747452v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:38,077] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:38,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg703a2cd6-6503-4662-bc25-5c7c28727722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:38,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg703a2cd6-6503-4662-bc25-5c7c28727722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:38,096] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:14:38,096] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:14:38,097] [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 rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	81.5076	628	1150	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	81.4532	677	1150	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	81.3877	620	1150	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	81.3619	645	1150	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	81.2881	572	1150	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	81.2024	601	1150	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	81.1097	659	1150	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	81.0052	585	1150	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	80.9799	575	1150	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	80.956	634	1150	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	80.7484	620	1150	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	80.4654	610	1150	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	79.8432	536	1150	95	below_threshold
Flavobacterium restrictum	strain=LB1R34	GCA_007097245.1	2594428	2594428	type	True	79.7146	556	1150	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	79.1056	421	1150	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	79.0628	412	1150	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	78.9599	429	1150	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.8898	394	1150	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.7569	414	1150	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.6684	400	1150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:38,100] [INFO] DFAST Taxonomy check result was written to GCF_027474525.2_ASM2747452v2_genomic.fna/tc_result.tsv
[2024-01-24 14:14:38,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:38,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:38,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg703a2cd6-6503-4662-bc25-5c7c28727722/dqc_reference/checkm_data
[2024-01-24 14:14:38,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:38,145] [INFO] Task started: CheckM
[2024-01-24 14:14:38,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027474525.2_ASM2747452v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027474525.2_ASM2747452v2_genomic.fna/checkm_input GCF_027474525.2_ASM2747452v2_genomic.fna/checkm_result
[2024-01-24 14:15:20,504] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:20,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:20,524] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:20,524] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:20,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027474525.2_ASM2747452v2_genomic.fna/markers.fasta)
[2024-01-24 14:15:20,525] [INFO] Task started: Blastn
[2024-01-24 14:15:20,525] [INFO] Running command: blastn -query GCF_027474525.2_ASM2747452v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg703a2cd6-6503-4662-bc25-5c7c28727722/dqc_reference/reference_markers_gtdb.fasta -out GCF_027474525.2_ASM2747452v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:21,634] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:21,638] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:21,638] [INFO] Target genome list was writen to GCF_027474525.2_ASM2747452v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:21,762] [INFO] Task started: fastANI
[2024-01-24 14:15:21,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a0c7a71-1864-43e9-9108-fcf299d149b8/GCF_027474525.2_ASM2747452v2_genomic.fna.gz --refList GCF_027474525.2_ASM2747452v2_genomic.fna/target_genomes_gtdb.txt --output GCF_027474525.2_ASM2747452v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:34,903] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:34,917] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:15:34,917] [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_003634825.1	s__Flavobacterium sp003634825	82.9604	700	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754315.1	s__Flavobacterium sp002754315	81.9863	701	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_000744835.1	s__Flavobacterium sp000744835	81.7215	690	1150	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	81.6683	692	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349195.1	s__Flavobacterium sp004349195	81.5256	626	1150	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	81.4634	676	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_003314435.2	s__Flavobacterium petrolei	81.3652	622	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_004349315.1	s__Flavobacterium sp004349315	81.3515	646	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
GCF_015752255.1	s__Flavobacterium sp015752255	81.2217	647	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112975.1	s__Flavobacterium xueshanense	80.9978	586	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349085.1	s__Flavobacterium caseinilyticum	80.9929	573	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	80.9634	632	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108015.1	s__Flavobacterium urumqiense	80.7894	615	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875765.1	s__Flavobacterium sp017875765	80.7458	607	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_007097385.1	s__Flavobacterium sp007097385	79.6281	530	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282055.1	s__Flavobacterium sp000282055	79.2882	467	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	78.9878	356	1150	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 14:15:34,919] [INFO] GTDB search result was written to GCF_027474525.2_ASM2747452v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:34,919] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:34,923] [INFO] DFAST_QC result json was written to GCF_027474525.2_ASM2747452v2_genomic.fna/dqc_result.json
[2024-01-24 14:15:34,923] [INFO] DFAST_QC completed!
[2024-01-24 14:15:34,923] [INFO] Total running time: 0h1m30s