[2024-01-25 18:53:35,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:35,530] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:35,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dcb58ea-0117-41c1-aba0-1d35e80bbde8/dqc_reference
[2024-01-25 18:53:36,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:36,619] [INFO] Task started: Prodigal
[2024-01-25 18:53:36,619] [INFO] Running command: gunzip -c /var/lib/cwl/stge2be3867-3e4f-4028-b73f-5b3f548741e6/GCF_013285155.1_ASM1328515v1_genomic.fna.gz | prodigal -d GCF_013285155.1_ASM1328515v1_genomic.fna/cds.fna -a GCF_013285155.1_ASM1328515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:46,091] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:46,092] [INFO] Task started: HMMsearch
[2024-01-25 18:53:46,092] [INFO] Running command: hmmsearch --tblout GCF_013285155.1_ASM1328515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dcb58ea-0117-41c1-aba0-1d35e80bbde8/dqc_reference/reference_markers.hmm GCF_013285155.1_ASM1328515v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:46,309] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:46,310] [INFO] Found 6/6 markers.
[2024-01-25 18:53:46,344] [INFO] Query marker FASTA was written to GCF_013285155.1_ASM1328515v1_genomic.fna/markers.fasta
[2024-01-25 18:53:46,345] [INFO] Task started: Blastn
[2024-01-25 18:53:46,345] [INFO] Running command: blastn -query GCF_013285155.1_ASM1328515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dcb58ea-0117-41c1-aba0-1d35e80bbde8/dqc_reference/reference_markers.fasta -out GCF_013285155.1_ASM1328515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:46,989] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:46,992] [INFO] Selected 14 target genomes.
[2024-01-25 18:53:46,992] [INFO] Target genome list was writen to GCF_013285155.1_ASM1328515v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:47,003] [INFO] Task started: fastANI
[2024-01-25 18:53:47,003] [INFO] Running command: fastANI --query /var/lib/cwl/stge2be3867-3e4f-4028-b73f-5b3f548741e6/GCF_013285155.1_ASM1328515v1_genomic.fna.gz --refList GCF_013285155.1_ASM1328515v1_genomic.fna/target_genomes.txt --output GCF_013285155.1_ASM1328515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:58,928] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:58,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dcb58ea-0117-41c1-aba0-1d35e80bbde8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:58,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dcb58ea-0117-41c1-aba0-1d35e80bbde8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:58,937] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:53:58,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:58,938] [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 undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	100.0	1371	1372	95	conclusive
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	89.8942	1045	1372	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	82.4726	813	1372	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	82.3318	826	1372	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	81.8775	819	1372	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	81.8001	855	1372	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	81.5391	837	1372	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	81.4363	803	1372	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	80.4803	698	1372	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.3972	198	1372	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.257	228	1372	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.2235	198	1372	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.0953	88	1372	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.0382	239	1372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:58,939] [INFO] DFAST Taxonomy check result was written to GCF_013285155.1_ASM1328515v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:58,940] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:58,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:58,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dcb58ea-0117-41c1-aba0-1d35e80bbde8/dqc_reference/checkm_data
[2024-01-25 18:53:58,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:58,981] [INFO] Task started: CheckM
[2024-01-25 18:53:58,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013285155.1_ASM1328515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013285155.1_ASM1328515v1_genomic.fna/checkm_input GCF_013285155.1_ASM1328515v1_genomic.fna/checkm_result
[2024-01-25 18:54:29,492] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:29,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:29,511] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:29,511] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:29,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013285155.1_ASM1328515v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:29,512] [INFO] Task started: Blastn
[2024-01-25 18:54:29,512] [INFO] Running command: blastn -query GCF_013285155.1_ASM1328515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dcb58ea-0117-41c1-aba0-1d35e80bbde8/dqc_reference/reference_markers_gtdb.fasta -out GCF_013285155.1_ASM1328515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:30,492] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:30,495] [INFO] Selected 11 target genomes.
[2024-01-25 18:54:30,495] [INFO] Target genome list was writen to GCF_013285155.1_ASM1328515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:30,505] [INFO] Task started: fastANI
[2024-01-25 18:54:30,505] [INFO] Running command: fastANI --query /var/lib/cwl/stge2be3867-3e4f-4028-b73f-5b3f548741e6/GCF_013285155.1_ASM1328515v1_genomic.fna.gz --refList GCF_013285155.1_ASM1328515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013285155.1_ASM1328515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:41,999] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:42,007] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:42,007] [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_013285155.1	s__Winogradskyella undariae	100.0	1371	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	conclusive
GCF_013403925.1	s__Winogradskyella wichelsiae	89.9062	1044	1372	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	82.4807	812	1372	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	82.3074	830	1372	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	81.8972	816	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	81.784	857	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_013403915.1	s__Winogradskyella pacifica	81.5345	796	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_013403955.1	s__Winogradskyella vidalii	81.5169	840	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337305.1	s__Winogradskyella arenosi	81.1104	762	1372	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	80.9146	747	1372	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	80.4751	701	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:42,009] [INFO] GTDB search result was written to GCF_013285155.1_ASM1328515v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:42,010] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:42,013] [INFO] DFAST_QC result json was written to GCF_013285155.1_ASM1328515v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:42,013] [INFO] DFAST_QC completed!
[2024-01-25 18:54:42,013] [INFO] Total running time: 0h1m6s