[2024-01-24 14:39:14,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b5c7ee6-39ad-4b11-bf4b-ccbce0c95a37/dqc_reference
[2024-01-24 14:39:16,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,140] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,140] [INFO] Running command: gunzip -c /var/lib/cwl/stga45d6aaa-2826-44cd-9dfa-6543bc156333/GCF_004365575.1_ASM436557v1_genomic.fna.gz | prodigal -d GCF_004365575.1_ASM436557v1_genomic.fna/cds.fna -a GCF_004365575.1_ASM436557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:19,515] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:19,516] [INFO] Task started: HMMsearch
[2024-01-24 14:39:19,516] [INFO] Running command: hmmsearch --tblout GCF_004365575.1_ASM436557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b5c7ee6-39ad-4b11-bf4b-ccbce0c95a37/dqc_reference/reference_markers.hmm GCF_004365575.1_ASM436557v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:19,764] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:19,766] [INFO] Found 6/6 markers.
[2024-01-24 14:39:19,801] [INFO] Query marker FASTA was written to GCF_004365575.1_ASM436557v1_genomic.fna/markers.fasta
[2024-01-24 14:39:19,801] [INFO] Task started: Blastn
[2024-01-24 14:39:19,802] [INFO] Running command: blastn -query GCF_004365575.1_ASM436557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b5c7ee6-39ad-4b11-bf4b-ccbce0c95a37/dqc_reference/reference_markers.fasta -out GCF_004365575.1_ASM436557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:20,468] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:20,471] [INFO] Selected 23 target genomes.
[2024-01-24 14:39:20,472] [INFO] Target genome list was writen to GCF_004365575.1_ASM436557v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:20,498] [INFO] Task started: fastANI
[2024-01-24 14:39:20,499] [INFO] Running command: fastANI --query /var/lib/cwl/stga45d6aaa-2826-44cd-9dfa-6543bc156333/GCF_004365575.1_ASM436557v1_genomic.fna.gz --refList GCF_004365575.1_ASM436557v1_genomic.fna/target_genomes.txt --output GCF_004365575.1_ASM436557v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:29,507] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:29,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b5c7ee6-39ad-4b11-bf4b-ccbce0c95a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:29,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b5c7ee6-39ad-4b11-bf4b-ccbce0c95a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:29,524] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:29,524] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:29,524] [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
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	75.8989	129	731	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	75.8247	146	731	95	below_threshold
Ilyobacter polytropus	strain=DSM 2926	GCA_000165505.1	167642	167642	type	True	75.7431	79	731	95	below_threshold
Fusobacterium pseudoperiodonticum	strain=KCOM 1259	GCA_002761955.1	2663009	2663009	type	True	75.6869	112	731	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	75.6691	147	731	95	below_threshold
Psychrilyobacter atlanticus	strain=DSM 19335	GCA_000426625.1	271091	271091	type	True	75.6466	116	731	95	below_threshold
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	75.602	185	731	95	below_threshold
Fusobacterium periodonticum	strain=ATCC 33693	GCA_000160475.1	860	860	suspected-type	True	75.5536	135	731	95	below_threshold
Streptobacillus felis	strain=131000547	GCA_001559775.1	1384509	1384509	type	True	75.5234	85	731	95	below_threshold
Cetobacterium ceti	strain=ATCC 700028	GCA_900167275.1	180163	180163	type	True	75.4984	146	731	95	below_threshold
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	75.4144	139	731	95	below_threshold
Caviibacter abscessus	strain=CCUG 39713	GCA_001517835.1	1766719	1766719	type	True	75.2801	78	731	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 9904	GCA_006165035.1	28198	28198	suspected-type	True	74.897	73	731	95	below_threshold
Aliarcobacter cryaerophilus	strain=ATCC 43158	GCA_003660105.1	28198	28198	suspected-type	True	74.886	74	731	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	74.7492	67	731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:29,527] [INFO] DFAST Taxonomy check result was written to GCF_004365575.1_ASM436557v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:29,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:29,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:29,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b5c7ee6-39ad-4b11-bf4b-ccbce0c95a37/dqc_reference/checkm_data
[2024-01-24 14:39:29,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:29,566] [INFO] Task started: CheckM
[2024-01-24 14:39:29,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365575.1_ASM436557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365575.1_ASM436557v1_genomic.fna/checkm_input GCF_004365575.1_ASM436557v1_genomic.fna/checkm_result
[2024-01-24 14:39:48,234] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:48,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:48,255] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:48,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:48,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365575.1_ASM436557v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:48,256] [INFO] Task started: Blastn
[2024-01-24 14:39:48,257] [INFO] Running command: blastn -query GCF_004365575.1_ASM436557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b5c7ee6-39ad-4b11-bf4b-ccbce0c95a37/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365575.1_ASM436557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:49,048] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:49,052] [INFO] Selected 17 target genomes.
[2024-01-24 14:39:49,052] [INFO] Target genome list was writen to GCF_004365575.1_ASM436557v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:49,064] [INFO] Task started: fastANI
[2024-01-24 14:39:49,065] [INFO] Running command: fastANI --query /var/lib/cwl/stga45d6aaa-2826-44cd-9dfa-6543bc156333/GCF_004365575.1_ASM436557v1_genomic.fna.gz --refList GCF_004365575.1_ASM436557v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365575.1_ASM436557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:57,076] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:57,096] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:57,097] [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_004365575.1	s__Hypnocyclicus thermotrophus	100.0	731	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Hypnocyclicus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017988045.1	s__JAFGUR01 sp017988045	76.0963	137	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__JAFGUR01	95.0	99.28	99.17	0.76	0.75	4	-
GCA_003973585.1	s__Psychrilyobacter sp003973585	76.0724	65	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938425.1	s__JAFGUR01 sp016938425	75.9599	132	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__JAFGUR01	95.0	99.62	99.62	0.87	0.87	2	-
GCF_016724785.1	s__Fusobacterium canifelinum	75.9066	130	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.22	98.13	0.90	0.87	3	-
GCA_000182945.1	s__Fusobacterium vincentii	75.8878	108	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.44	96.10	0.85	0.73	18	-
GCF_000165505.1	s__Ilyobacter polytropus	75.8121	74	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Ilyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766645.1	s__Cetobacterium_A sp900766645	75.8079	86	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019012925.1	s__Fusobacterium_A sp019012925	75.7999	82	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014250675.1	s__Cetobacterium_A sp014250675	75.7468	119	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905193185.1	s__Fusobacterium_B sp900554355	75.7416	121	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B	95.0	99.50	99.01	0.96	0.94	3	-
GCF_000158195.2	s__Fusobacterium_A mortiferum	75.7243	148	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.16	98.67	0.92	0.88	9	-
GCF_900683735.1	s__Fusobacterium_A ulcerans_A	75.6777	150	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.86	98.73	0.94	0.93	4	-
GCA_905216205.1	s__Cetobacterium_A sp905216205	75.607	143	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342785.1	s__Psychrilyobacter sp002342785	75.4811	173	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000479045.1	s__Cetobacterium_A somerae	75.4453	134	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	99.23	98.47	0.92	0.85	3	-
GCF_003391055.1	s__Psychrilyobacter sp003391055	75.383	79	731	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter	95.0	100.00	100.00	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:57,098] [INFO] GTDB search result was written to GCF_004365575.1_ASM436557v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:57,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:57,103] [INFO] DFAST_QC result json was written to GCF_004365575.1_ASM436557v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:57,104] [INFO] DFAST_QC completed!
[2024-01-24 14:39:57,104] [INFO] Total running time: 0h0m42s