[2024-01-24 15:32:05,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg24e5b000-1fc0-47ba-a675-6e837b036dc2/dqc_reference
[2024-01-24 15:32:06,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:06,720] [INFO] Task started: Prodigal
[2024-01-24 15:32:06,720] [INFO] Running command: gunzip -c /var/lib/cwl/stgac4743a3-2387-4176-8624-83a10b2a2062/GCF_009740285.1_ASM974028v1_genomic.fna.gz | prodigal -d GCF_009740285.1_ASM974028v1_genomic.fna/cds.fna -a GCF_009740285.1_ASM974028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:35,806] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:35,807] [INFO] Task started: HMMsearch
[2024-01-24 15:32:35,807] [INFO] Running command: hmmsearch --tblout GCF_009740285.1_ASM974028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24e5b000-1fc0-47ba-a675-6e837b036dc2/dqc_reference/reference_markers.hmm GCF_009740285.1_ASM974028v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:36,105] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:36,106] [INFO] Found 6/6 markers.
[2024-01-24 15:32:36,145] [INFO] Query marker FASTA was written to GCF_009740285.1_ASM974028v1_genomic.fna/markers.fasta
[2024-01-24 15:32:36,146] [INFO] Task started: Blastn
[2024-01-24 15:32:36,146] [INFO] Running command: blastn -query GCF_009740285.1_ASM974028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24e5b000-1fc0-47ba-a675-6e837b036dc2/dqc_reference/reference_markers.fasta -out GCF_009740285.1_ASM974028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:36,741] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:36,746] [INFO] Selected 23 target genomes.
[2024-01-24 15:32:36,746] [INFO] Target genome list was writen to GCF_009740285.1_ASM974028v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:36,788] [INFO] Task started: fastANI
[2024-01-24 15:32:36,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgac4743a3-2387-4176-8624-83a10b2a2062/GCF_009740285.1_ASM974028v1_genomic.fna.gz --refList GCF_009740285.1_ASM974028v1_genomic.fna/target_genomes.txt --output GCF_009740285.1_ASM974028v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:55,938] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:55,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24e5b000-1fc0-47ba-a675-6e837b036dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:55,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24e5b000-1fc0-47ba-a675-6e837b036dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:55,964] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:32:55,964] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:55,964] [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
Phnomibacter ginsenosidimutans	strain=SB-02	GCA_009740285.1	2676868	2676868	type	True	100.0	1457	1457	95	conclusive
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	77.3578	73	1457	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.8453	69	1457	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.7851	131	1457	95	below_threshold
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	76.7273	55	1457	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.5047	67	1457	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.5014	81	1457	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.4118	71	1457	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	76.2551	96	1457	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.2423	103	1457	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.2253	87	1457	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.0547	59	1457	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.0228	57	1457	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.7323	73	1457	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	75.7303	64	1457	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.7268	57	1457	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.7146	73	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:55,966] [INFO] DFAST Taxonomy check result was written to GCF_009740285.1_ASM974028v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:55,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:55,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:55,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24e5b000-1fc0-47ba-a675-6e837b036dc2/dqc_reference/checkm_data
[2024-01-24 15:32:55,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:56,012] [INFO] Task started: CheckM
[2024-01-24 15:32:56,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009740285.1_ASM974028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009740285.1_ASM974028v1_genomic.fna/checkm_input GCF_009740285.1_ASM974028v1_genomic.fna/checkm_result
[2024-01-24 15:34:14,933] [INFO] Task succeeded: CheckM
[2024-01-24 15:34:14,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:34:14,955] [INFO] ===== Completeness check finished =====
[2024-01-24 15:34:14,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:34:14,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009740285.1_ASM974028v1_genomic.fna/markers.fasta)
[2024-01-24 15:34:14,956] [INFO] Task started: Blastn
[2024-01-24 15:34:14,957] [INFO] Running command: blastn -query GCF_009740285.1_ASM974028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24e5b000-1fc0-47ba-a675-6e837b036dc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009740285.1_ASM974028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:34:15,746] [INFO] Task succeeded: Blastn
[2024-01-24 15:34:15,751] [INFO] Selected 23 target genomes.
[2024-01-24 15:34:15,751] [INFO] Target genome list was writen to GCF_009740285.1_ASM974028v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:34:15,802] [INFO] Task started: fastANI
[2024-01-24 15:34:15,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgac4743a3-2387-4176-8624-83a10b2a2062/GCF_009740285.1_ASM974028v1_genomic.fna.gz --refList GCF_009740285.1_ASM974028v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009740285.1_ASM974028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:34:33,490] [INFO] Task succeeded: fastANI
[2024-01-24 15:34:33,509] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:34:33,509] [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_009740285.1	s__Phnomibacter ginsenosidimutans	100.0	1457	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Phnomibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014332695.1	s__Flavihumibacter stibioxidans	77.3578	73	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830055.1	s__Lacibacter cauensis	76.8982	132	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595685.1	s__Flavihumibacter sp018595685	76.749	68	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332885.2	s__Paracnuella aquatica	76.6836	114	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	-
GCA_016722465.1	s__Ferruginibacter sp016722465	76.351	69	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.3462	79	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.323	88	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183765.1	s__Sediminibacterium sp016183765	76.3188	75	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097095.1	s__Filimonas sp003097095	76.2598	80	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292575.1	s__Phnomibacter sp004292575	76.2321	110	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Phnomibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303335.1	s__Ferruginibacter sp017303335	76.2136	64	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.06	98.06	0.96	0.96	2	-
GCA_001898485.1	s__46-32 sp001898485	76.208	73	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	99.14	98.30	0.96	0.92	3	-
GCA_002399735.1	s__Terrimonas sp002399735	75.8351	67	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013106755.1	s__Panacibacter sp013106755	75.7146	73	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787265.1	s__Flavihumibacter sp016787265	75.4912	61	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:34:33,516] [INFO] GTDB search result was written to GCF_009740285.1_ASM974028v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:34:33,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:34:33,520] [INFO] DFAST_QC result json was written to GCF_009740285.1_ASM974028v1_genomic.fna/dqc_result.json
[2024-01-24 15:34:33,520] [INFO] DFAST_QC completed!
[2024-01-24 15:34:33,520] [INFO] Total running time: 0h2m28s