[2024-01-24 12:31:21,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,187] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f3db1c1-43a1-494c-a45f-eb683d1b07fd/dqc_reference
[2024-01-24 12:31:22,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,514] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg76d620cf-d96c-47f6-b6eb-c39ab1226702/GCF_009709615.1_ASM970961v1_genomic.fna.gz | prodigal -d GCF_009709615.1_ASM970961v1_genomic.fna/cds.fna -a GCF_009709615.1_ASM970961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:35,865] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:35,865] [INFO] Task started: HMMsearch
[2024-01-24 12:31:35,865] [INFO] Running command: hmmsearch --tblout GCF_009709615.1_ASM970961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f3db1c1-43a1-494c-a45f-eb683d1b07fd/dqc_reference/reference_markers.hmm GCF_009709615.1_ASM970961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:36,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:36,095] [INFO] Found 6/6 markers.
[2024-01-24 12:31:36,125] [INFO] Query marker FASTA was written to GCF_009709615.1_ASM970961v1_genomic.fna/markers.fasta
[2024-01-24 12:31:36,126] [INFO] Task started: Blastn
[2024-01-24 12:31:36,126] [INFO] Running command: blastn -query GCF_009709615.1_ASM970961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f3db1c1-43a1-494c-a45f-eb683d1b07fd/dqc_reference/reference_markers.fasta -out GCF_009709615.1_ASM970961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:36,821] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:36,824] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:36,825] [INFO] Target genome list was writen to GCF_009709615.1_ASM970961v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:36,833] [INFO] Task started: fastANI
[2024-01-24 12:31:36,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg76d620cf-d96c-47f6-b6eb-c39ab1226702/GCF_009709615.1_ASM970961v1_genomic.fna.gz --refList GCF_009709615.1_ASM970961v1_genomic.fna/target_genomes.txt --output GCF_009709615.1_ASM970961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:50,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:50,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f3db1c1-43a1-494c-a45f-eb683d1b07fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:50,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f3db1c1-43a1-494c-a45f-eb683d1b07fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:50,909] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:50,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:50,909] [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 ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	100.0	1153	1153	95	conclusive
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	79.5646	520	1153	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	79.243	535	1153	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	79.0587	441	1153	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.0359	568	1153	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.0358	568	1153	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	78.5125	417	1153	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.4992	418	1153	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.4326	427	1153	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.2197	440	1153	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	78.1967	481	1153	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	78.0471	426	1153	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.8356	300	1153	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.8285	311	1153	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.8012	313	1153	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.5819	261	1153	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.5215	213	1153	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.3157	217	1153	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.186	181	1153	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.115	177	1153	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.9005	180	1153	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:50,912] [INFO] DFAST Taxonomy check result was written to GCF_009709615.1_ASM970961v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:50,913] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:50,913] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:50,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f3db1c1-43a1-494c-a45f-eb683d1b07fd/dqc_reference/checkm_data
[2024-01-24 12:31:50,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:50,951] [INFO] Task started: CheckM
[2024-01-24 12:31:50,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009709615.1_ASM970961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009709615.1_ASM970961v1_genomic.fna/checkm_input GCF_009709615.1_ASM970961v1_genomic.fna/checkm_result
[2024-01-24 12:32:29,337] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:29,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.60%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:29,362] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:29,362] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:29,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009709615.1_ASM970961v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:29,363] [INFO] Task started: Blastn
[2024-01-24 12:32:29,363] [INFO] Running command: blastn -query GCF_009709615.1_ASM970961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f3db1c1-43a1-494c-a45f-eb683d1b07fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_009709615.1_ASM970961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:30,252] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:30,255] [INFO] Selected 19 target genomes.
[2024-01-24 12:32:30,255] [INFO] Target genome list was writen to GCF_009709615.1_ASM970961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:30,283] [INFO] Task started: fastANI
[2024-01-24 12:32:30,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg76d620cf-d96c-47f6-b6eb-c39ab1226702/GCF_009709615.1_ASM970961v1_genomic.fna.gz --refList GCF_009709615.1_ASM970961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009709615.1_ASM970961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:44,127] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:44,142] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:44,142] [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_009709615.1	s__Winogradskyella ouciana	100.0	1153	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	conclusive
GCF_005869935.1	s__Winogradskyella algicola	79.5646	520	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203985.1	s__Winogradskyella sp019203985	79.555	556	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	79.1448	535	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722255.1	s__Winogradskyella sp002722255	79.0876	451	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_013403975.1	s__Winogradskyella ursingii	79.0533	441	1153	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	79.0399	568	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002682935.1	s__Winogradskyella sp002682935	78.9255	512	1153	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	78.8743	458	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	78.7822	528	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	78.7775	543	1153	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	78.5405	475	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394655.1	s__Winogradskyella schleiferi	78.5336	495	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260205.1	s__Winogradskyella tangerina	78.5125	417	1153	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	78.4647	438	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403865.1	s__Winogradskyella costae	78.4604	426	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213975.1	s__Winogradskyella sp013213975	78.3195	386	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394595.1	s__Winogradskyella forsetii	78.204	480	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.73	96.59	0.91	0.86	4	-
GCF_004346845.1	s__Winogradskyella wandonensis	77.8079	314	1153	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:44,144] [INFO] GTDB search result was written to GCF_009709615.1_ASM970961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:44,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:44,149] [INFO] DFAST_QC result json was written to GCF_009709615.1_ASM970961v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:44,149] [INFO] DFAST_QC completed!
[2024-01-24 12:32:44,149] [INFO] Total running time: 0h1m23s