[2024-01-24 14:05:36,438] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,445] [INFO] DQC Reference Directory: /var/lib/cwl/stge7dc48dc-80fa-4951-a10a-cf5f506cfd11/dqc_reference
[2024-01-24 14:05:37,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,884] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,884] [INFO] Running command: gunzip -c /var/lib/cwl/stga818d0cf-571e-4b5d-8ff0-5ad300e4752f/GCF_013394595.1_ASM1339459v1_genomic.fna.gz | prodigal -d GCF_013394595.1_ASM1339459v1_genomic.fna/cds.fna -a GCF_013394595.1_ASM1339459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:55,497] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:55,497] [INFO] Task started: HMMsearch
[2024-01-24 14:05:55,498] [INFO] Running command: hmmsearch --tblout GCF_013394595.1_ASM1339459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7dc48dc-80fa-4951-a10a-cf5f506cfd11/dqc_reference/reference_markers.hmm GCF_013394595.1_ASM1339459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:55,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:55,797] [INFO] Found 6/6 markers.
[2024-01-24 14:05:55,839] [INFO] Query marker FASTA was written to GCF_013394595.1_ASM1339459v1_genomic.fna/markers.fasta
[2024-01-24 14:05:55,840] [INFO] Task started: Blastn
[2024-01-24 14:05:55,840] [INFO] Running command: blastn -query GCF_013394595.1_ASM1339459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7dc48dc-80fa-4951-a10a-cf5f506cfd11/dqc_reference/reference_markers.fasta -out GCF_013394595.1_ASM1339459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:56,560] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:56,563] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:56,564] [INFO] Target genome list was writen to GCF_013394595.1_ASM1339459v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:56,570] [INFO] Task started: fastANI
[2024-01-24 14:05:56,570] [INFO] Running command: fastANI --query /var/lib/cwl/stga818d0cf-571e-4b5d-8ff0-5ad300e4752f/GCF_013394595.1_ASM1339459v1_genomic.fna.gz --refList GCF_013394595.1_ASM1339459v1_genomic.fna/target_genomes.txt --output GCF_013394595.1_ASM1339459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:11,603] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:11,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7dc48dc-80fa-4951-a10a-cf5f506cfd11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:11,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7dc48dc-80fa-4951-a10a-cf5f506cfd11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:11,618] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:11,619] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:11,619] [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 forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	100.0	1502	1504	95	conclusive
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	90.4268	1159	1504	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	79.939	661	1504	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	79.9253	712	1504	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	79.9194	689	1504	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	79.6053	641	1504	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	79.5906	630	1504	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	79.4809	658	1504	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	79.454	581	1504	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	79.3688	638	1504	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	79.3578	563	1504	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	79.3203	579	1504	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.3936	186	1504	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.3638	253	1504	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.9856	156	1504	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.9358	60	1504	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.9054	140	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:11,623] [INFO] DFAST Taxonomy check result was written to GCF_013394595.1_ASM1339459v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:11,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:11,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:11,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7dc48dc-80fa-4951-a10a-cf5f506cfd11/dqc_reference/checkm_data
[2024-01-24 14:06:11,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:11,673] [INFO] Task started: CheckM
[2024-01-24 14:06:11,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013394595.1_ASM1339459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013394595.1_ASM1339459v1_genomic.fna/checkm_input GCF_013394595.1_ASM1339459v1_genomic.fna/checkm_result
[2024-01-24 14:07:03,668] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:03,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:03,690] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:03,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:03,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013394595.1_ASM1339459v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:03,692] [INFO] Task started: Blastn
[2024-01-24 14:07:03,692] [INFO] Running command: blastn -query GCF_013394595.1_ASM1339459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7dc48dc-80fa-4951-a10a-cf5f506cfd11/dqc_reference/reference_markers_gtdb.fasta -out GCF_013394595.1_ASM1339459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:04,672] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:04,676] [INFO] Selected 16 target genomes.
[2024-01-24 14:07:04,676] [INFO] Target genome list was writen to GCF_013394595.1_ASM1339459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:04,698] [INFO] Task started: fastANI
[2024-01-24 14:07:04,699] [INFO] Running command: fastANI --query /var/lib/cwl/stga818d0cf-571e-4b5d-8ff0-5ad300e4752f/GCF_013394595.1_ASM1339459v1_genomic.fna.gz --refList GCF_013394595.1_ASM1339459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013394595.1_ASM1339459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:18,177] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:18,191] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:18,191] [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_013394595.1	s__Winogradskyella forsetii	100.0	1502	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.73	96.59	0.91	0.86	4	conclusive
GCF_013394655.1	s__Winogradskyella schleiferi	90.4396	1159	1504	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	80.1431	739	1504	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	80.0625	702	1504	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	79.9341	662	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099995.1	s__Winogradskyella thalassocola	79.9329	711	1504	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	79.922	687	1504	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	79.8865	651	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_015645385.1	s__Winogradskyella sp015645385	79.6097	640	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	79.5906	630	1504	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	79.4809	658	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	79.4517	581	1504	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	79.3625	638	1504	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	79.3113	580	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013285155.1	s__Winogradskyella undariae	79.0899	569	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_000828715.1	s__Winogradskyella sp000828715	78.6762	472	1504	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 14:07:18,192] [INFO] GTDB search result was written to GCF_013394595.1_ASM1339459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:18,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:18,196] [INFO] DFAST_QC result json was written to GCF_013394595.1_ASM1339459v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:18,197] [INFO] DFAST_QC completed!
[2024-01-24 14:07:18,197] [INFO] Total running time: 0h1m42s