[2024-01-24 13:40:40,166] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:40,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:40,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cf575f0-9d81-42a6-a58e-96f6ae934c55/dqc_reference
[2024-01-24 13:40:41,434] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:41,435] [INFO] Task started: Prodigal
[2024-01-24 13:40:41,435] [INFO] Running command: gunzip -c /var/lib/cwl/stg68f0558d-7f4f-43e3-bf43-93e7d637d9b5/GCF_014651315.1_ASM1465131v1_genomic.fna.gz | prodigal -d GCF_014651315.1_ASM1465131v1_genomic.fna/cds.fna -a GCF_014651315.1_ASM1465131v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:52,638] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:52,639] [INFO] Task started: HMMsearch
[2024-01-24 13:40:52,639] [INFO] Running command: hmmsearch --tblout GCF_014651315.1_ASM1465131v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cf575f0-9d81-42a6-a58e-96f6ae934c55/dqc_reference/reference_markers.hmm GCF_014651315.1_ASM1465131v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:52,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:52,960] [INFO] Found 6/6 markers.
[2024-01-24 13:40:52,988] [INFO] Query marker FASTA was written to GCF_014651315.1_ASM1465131v1_genomic.fna/markers.fasta
[2024-01-24 13:40:52,988] [INFO] Task started: Blastn
[2024-01-24 13:40:52,988] [INFO] Running command: blastn -query GCF_014651315.1_ASM1465131v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf575f0-9d81-42a6-a58e-96f6ae934c55/dqc_reference/reference_markers.fasta -out GCF_014651315.1_ASM1465131v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:53,713] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:53,717] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:53,717] [INFO] Target genome list was writen to GCF_014651315.1_ASM1465131v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:53,725] [INFO] Task started: fastANI
[2024-01-24 13:40:53,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg68f0558d-7f4f-43e3-bf43-93e7d637d9b5/GCF_014651315.1_ASM1465131v1_genomic.fna.gz --refList GCF_014651315.1_ASM1465131v1_genomic.fna/target_genomes.txt --output GCF_014651315.1_ASM1465131v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:08,301] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:08,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cf575f0-9d81-42a6-a58e-96f6ae934c55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:08,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cf575f0-9d81-42a6-a58e-96f6ae934c55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:08,315] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:08,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:08,315] [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
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	100.0	1098	1099	95	conclusive
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	99.9941	1098	1099	95	conclusive
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	79.6104	562	1099	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	79.5522	542	1099	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	79.4064	556	1099	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	79.3848	514	1099	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	79.3109	501	1099	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	79.3021	496	1099	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	79.2587	516	1099	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	79.0683	510	1099	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.9852	515	1099	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.0945	341	1099	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.8147	358	1099	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.455	182	1099	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.3855	253	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:08,317] [INFO] DFAST Taxonomy check result was written to GCF_014651315.1_ASM1465131v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:08,318] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:08,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:08,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cf575f0-9d81-42a6-a58e-96f6ae934c55/dqc_reference/checkm_data
[2024-01-24 13:41:08,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:08,357] [INFO] Task started: CheckM
[2024-01-24 13:41:08,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651315.1_ASM1465131v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651315.1_ASM1465131v1_genomic.fna/checkm_input GCF_014651315.1_ASM1465131v1_genomic.fna/checkm_result
[2024-01-24 13:41:45,814] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:45,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,908] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:45,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:45,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651315.1_ASM1465131v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:45,909] [INFO] Task started: Blastn
[2024-01-24 13:41:45,909] [INFO] Running command: blastn -query GCF_014651315.1_ASM1465131v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf575f0-9d81-42a6-a58e-96f6ae934c55/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651315.1_ASM1465131v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:47,052] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:47,055] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:47,055] [INFO] Target genome list was writen to GCF_014651315.1_ASM1465131v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:47,067] [INFO] Task started: fastANI
[2024-01-24 13:41:47,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg68f0558d-7f4f-43e3-bf43-93e7d637d9b5/GCF_014651315.1_ASM1465131v1_genomic.fna.gz --refList GCF_014651315.1_ASM1465131v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651315.1_ASM1465131v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:58,769] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:58,787] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:58,787] [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_003217215.1	s__Winogradskyella epiphytica	99.9941	1098	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_013403915.1	s__Winogradskyella pacifica	79.6512	532	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_900099995.1	s__Winogradskyella thalassocola	79.615	562	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	79.584	539	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427335.1	s__Winogradskyella psychrotolerans	79.5664	543	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645385.1	s__Winogradskyella sp015645385	79.3962	558	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	79.3865	545	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	79.3706	516	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013285155.1	s__Winogradskyella undariae	79.3109	501	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_013403865.1	s__Winogradskyella costae	79.3028	495	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	79.2258	520	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013403955.1	s__Winogradskyella vidalii	79.0809	509	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	78.7467	447	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000828715.1	s__Winogradskyella sp000828715	78.5035	386	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	78.1746	376	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518485.1	s__Olleya marilimosa	77.3737	254	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,789] [INFO] GTDB search result was written to GCF_014651315.1_ASM1465131v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:58,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:58,793] [INFO] DFAST_QC result json was written to GCF_014651315.1_ASM1465131v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:58,793] [INFO] DFAST_QC completed!
[2024-01-24 13:41:58,794] [INFO] Total running time: 0h1m19s