[2024-01-24 13:18:46,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,449] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7eee0a8-2e6d-4411-90f1-4fdacf9fc5c5/dqc_reference
[2024-01-24 13:18:47,705] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,706] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,706] [INFO] Running command: gunzip -c /var/lib/cwl/stg19a1075b-df1a-4ced-9b58-4dd5674953c7/GCF_013403985.1_ASM1340398v1_genomic.fna.gz | prodigal -d GCF_013403985.1_ASM1340398v1_genomic.fna/cds.fna -a GCF_013403985.1_ASM1340398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:59,905] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:59,906] [INFO] Task started: HMMsearch
[2024-01-24 13:18:59,906] [INFO] Running command: hmmsearch --tblout GCF_013403985.1_ASM1340398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7eee0a8-2e6d-4411-90f1-4fdacf9fc5c5/dqc_reference/reference_markers.hmm GCF_013403985.1_ASM1340398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:00,195] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:00,196] [INFO] Found 6/6 markers.
[2024-01-24 13:19:00,231] [INFO] Query marker FASTA was written to GCF_013403985.1_ASM1340398v1_genomic.fna/markers.fasta
[2024-01-24 13:19:00,232] [INFO] Task started: Blastn
[2024-01-24 13:19:00,232] [INFO] Running command: blastn -query GCF_013403985.1_ASM1340398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7eee0a8-2e6d-4411-90f1-4fdacf9fc5c5/dqc_reference/reference_markers.fasta -out GCF_013403985.1_ASM1340398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:00,963] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:00,967] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:00,968] [INFO] Target genome list was writen to GCF_013403985.1_ASM1340398v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:00,979] [INFO] Task started: fastANI
[2024-01-24 13:19:00,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg19a1075b-df1a-4ced-9b58-4dd5674953c7/GCF_013403985.1_ASM1340398v1_genomic.fna.gz --refList GCF_013403985.1_ASM1340398v1_genomic.fna/target_genomes.txt --output GCF_013403985.1_ASM1340398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:14,590] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:14,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7eee0a8-2e6d-4411-90f1-4fdacf9fc5c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:14,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7eee0a8-2e6d-4411-90f1-4fdacf9fc5c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:14,604] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:14,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:14,604] [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 ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	100.0	1323	1323	95	conclusive
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	83.6103	890	1323	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	83.4532	971	1323	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	82.8935	913	1323	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	82.6718	823	1323	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	82.3634	881	1323	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	82.287	832	1323	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	81.223	793	1323	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	81.0599	747	1323	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	80.8418	763	1323	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	80.0647	687	1323	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.2725	260	1323	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.26	211	1323	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2051	241	1323	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.9737	230	1323	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.433	130	1323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:14,606] [INFO] DFAST Taxonomy check result was written to GCF_013403985.1_ASM1340398v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:14,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:14,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:14,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7eee0a8-2e6d-4411-90f1-4fdacf9fc5c5/dqc_reference/checkm_data
[2024-01-24 13:19:14,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:14,650] [INFO] Task started: CheckM
[2024-01-24 13:19:14,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013403985.1_ASM1340398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013403985.1_ASM1340398v1_genomic.fna/checkm_input GCF_013403985.1_ASM1340398v1_genomic.fna/checkm_result
[2024-01-24 13:19:51,572] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:51,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:51,590] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:51,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:51,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013403985.1_ASM1340398v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:51,591] [INFO] Task started: Blastn
[2024-01-24 13:19:51,591] [INFO] Running command: blastn -query GCF_013403985.1_ASM1340398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7eee0a8-2e6d-4411-90f1-4fdacf9fc5c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_013403985.1_ASM1340398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:52,611] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:52,614] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:52,614] [INFO] Target genome list was writen to GCF_013403985.1_ASM1340398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:52,645] [INFO] Task started: fastANI
[2024-01-24 13:19:52,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg19a1075b-df1a-4ced-9b58-4dd5674953c7/GCF_013403985.1_ASM1340398v1_genomic.fna.gz --refList GCF_013403985.1_ASM1340398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013403985.1_ASM1340398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:02,983] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:02,993] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:02,994] [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_013403985.1	s__Winogradskyella ludwigii	100.0	1323	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013404085.1	s__Winogradskyella helgolandensis	83.4409	974	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_000427335.1	s__Winogradskyella psychrotolerans	82.8953	913	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	82.6386	876	1323	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	82.3392	884	1323	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	82.3198	877	1323	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	82.3029	830	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	81.9341	801	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	81.7977	872	1323	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	81.2327	793	1323	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	80.8219	766	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:02,996] [INFO] GTDB search result was written to GCF_013403985.1_ASM1340398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:02,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:03,004] [INFO] DFAST_QC result json was written to GCF_013403985.1_ASM1340398v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:03,004] [INFO] DFAST_QC completed!
[2024-01-24 13:20:03,004] [INFO] Total running time: 0h1m17s