[2024-01-24 15:27:12,512] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,521] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaa16c9b-5a83-41e8-a458-9731cd0669c1/dqc_reference
[2024-01-24 15:27:13,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:13,908] [INFO] Task started: Prodigal
[2024-01-24 15:27:13,908] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf40f4df-d96f-4c43-ab51-5ac4b79bae87/GCF_003387355.1_ASM338735v1_genomic.fna.gz | prodigal -d GCF_003387355.1_ASM338735v1_genomic.fna/cds.fna -a GCF_003387355.1_ASM338735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:25,818] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:25,818] [INFO] Task started: HMMsearch
[2024-01-24 15:27:25,818] [INFO] Running command: hmmsearch --tblout GCF_003387355.1_ASM338735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaa16c9b-5a83-41e8-a458-9731cd0669c1/dqc_reference/reference_markers.hmm GCF_003387355.1_ASM338735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:26,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:26,252] [INFO] Found 6/6 markers.
[2024-01-24 15:27:26,296] [INFO] Query marker FASTA was written to GCF_003387355.1_ASM338735v1_genomic.fna/markers.fasta
[2024-01-24 15:27:26,297] [INFO] Task started: Blastn
[2024-01-24 15:27:26,297] [INFO] Running command: blastn -query GCF_003387355.1_ASM338735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa16c9b-5a83-41e8-a458-9731cd0669c1/dqc_reference/reference_markers.fasta -out GCF_003387355.1_ASM338735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:27,089] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:27,093] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:27,093] [INFO] Target genome list was writen to GCF_003387355.1_ASM338735v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:27,103] [INFO] Task started: fastANI
[2024-01-24 15:27:27,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf40f4df-d96f-4c43-ab51-5ac4b79bae87/GCF_003387355.1_ASM338735v1_genomic.fna.gz --refList GCF_003387355.1_ASM338735v1_genomic.fna/target_genomes.txt --output GCF_003387355.1_ASM338735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:40,623] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:40,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaa16c9b-5a83-41e8-a458-9731cd0669c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:40,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaa16c9b-5a83-41e8-a458-9731cd0669c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:40,637] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:40,637] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:40,637] [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 sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	100.0	1250	1251	95	conclusive
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	83.0703	910	1251	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	82.6835	931	1251	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	81.801	850	1251	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	81.7871	829	1251	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	80.869	759	1251	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	80.482	701	1251	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	80.2498	640	1251	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	80.2172	661	1251	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	80.209	718	1251	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	80.0595	619	1251	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.6381	275	1251	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.3613	226	1251	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3256	215	1251	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2494	179	1251	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.1129	180	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:40,639] [INFO] DFAST Taxonomy check result was written to GCF_003387355.1_ASM338735v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:40,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:40,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:40,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaa16c9b-5a83-41e8-a458-9731cd0669c1/dqc_reference/checkm_data
[2024-01-24 15:27:40,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:40,679] [INFO] Task started: CheckM
[2024-01-24 15:27:40,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003387355.1_ASM338735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003387355.1_ASM338735v1_genomic.fna/checkm_input GCF_003387355.1_ASM338735v1_genomic.fna/checkm_result
[2024-01-24 15:28:18,981] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:18,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:19,013] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:19,013] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:19,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003387355.1_ASM338735v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:19,014] [INFO] Task started: Blastn
[2024-01-24 15:28:19,015] [INFO] Running command: blastn -query GCF_003387355.1_ASM338735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa16c9b-5a83-41e8-a458-9731cd0669c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003387355.1_ASM338735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:20,032] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:20,035] [INFO] Selected 11 target genomes.
[2024-01-24 15:28:20,035] [INFO] Target genome list was writen to GCF_003387355.1_ASM338735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:20,042] [INFO] Task started: fastANI
[2024-01-24 15:28:20,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf40f4df-d96f-4c43-ab51-5ac4b79bae87/GCF_003387355.1_ASM338735v1_genomic.fna.gz --refList GCF_003387355.1_ASM338735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003387355.1_ASM338735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:30,259] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:30,276] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:30,276] [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_003387355.1	s__Winogradskyella sediminis	100.0	1250	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	conclusive
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	83.6324	911	1251	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	83.0923	909	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	82.721	792	1251	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	82.6674	935	1251	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	81.7894	852	1251	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	81.7843	847	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_013403865.1	s__Winogradskyella costae	81.7789	830	1251	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	81.0053	719	1251	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	80.2412	658	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	80.21	718	1251	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 15:28:30,278] [INFO] GTDB search result was written to GCF_003387355.1_ASM338735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:30,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:30,283] [INFO] DFAST_QC result json was written to GCF_003387355.1_ASM338735v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:30,283] [INFO] DFAST_QC completed!
[2024-01-24 15:28:30,283] [INFO] Total running time: 0h1m18s