[2024-01-24 13:09:50,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:50,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:50,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg0575b5fd-8756-4252-b541-e367e9deace7/dqc_reference
[2024-01-24 13:09:52,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:52,220] [INFO] Task started: Prodigal
[2024-01-24 13:09:52,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ac6966a-6158-4564-9352-19a5a50d15ae/GCF_004364575.1_ASM436457v1_genomic.fna.gz | prodigal -d GCF_004364575.1_ASM436457v1_genomic.fna/cds.fna -a GCF_004364575.1_ASM436457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:03,247] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:03,247] [INFO] Task started: HMMsearch
[2024-01-24 13:10:03,247] [INFO] Running command: hmmsearch --tblout GCF_004364575.1_ASM436457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0575b5fd-8756-4252-b541-e367e9deace7/dqc_reference/reference_markers.hmm GCF_004364575.1_ASM436457v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:03,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:03,544] [INFO] Found 6/6 markers.
[2024-01-24 13:10:03,582] [INFO] Query marker FASTA was written to GCF_004364575.1_ASM436457v1_genomic.fna/markers.fasta
[2024-01-24 13:10:03,582] [INFO] Task started: Blastn
[2024-01-24 13:10:03,582] [INFO] Running command: blastn -query GCF_004364575.1_ASM436457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0575b5fd-8756-4252-b541-e367e9deace7/dqc_reference/reference_markers.fasta -out GCF_004364575.1_ASM436457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:04,293] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:04,297] [INFO] Selected 26 target genomes.
[2024-01-24 13:10:04,297] [INFO] Target genome list was writen to GCF_004364575.1_ASM436457v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:04,308] [INFO] Task started: fastANI
[2024-01-24 13:10:04,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ac6966a-6158-4564-9352-19a5a50d15ae/GCF_004364575.1_ASM436457v1_genomic.fna.gz --refList GCF_004364575.1_ASM436457v1_genomic.fna/target_genomes.txt --output GCF_004364575.1_ASM436457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:20,589] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:20,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0575b5fd-8756-4252-b541-e367e9deace7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:20,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0575b5fd-8756-4252-b541-e367e9deace7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:20,608] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:20,609] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:20,609] [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
Myroides indicus	strain=DSM 28213	GCA_004364575.1	1323422	1323422	type	True	100.0	979	981	95	conclusive
Myroides profundi	strain=D25	GCA_000833025.1	480520	480520	type	True	79.3194	173	981	95	below_threshold
Myroides odoratimimus subsp. xuanwuensis	strain=DSM 27251	GCA_900142635.1	1324934	76832	type	True	79.3087	181	981	95	below_threshold
Myroides albus	strain=BIT-d1	GCA_009711045.1	2562892	2562892	type	True	79.1923	192	981	95	below_threshold
Myroides odoratus	strain=DSM 2801	GCA_000243275.1	256	256	type	True	78.7327	229	981	95	below_threshold
Myroides odoratus	strain=NCTC11036	GCA_900453865.1	256	256	type	True	78.7108	225	981	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	78.6408	177	981	95	below_threshold
Myroides odoratus	strain=FDAARGOS_1131	GCA_016726985.1	256	256	type	True	78.6329	231	981	95	below_threshold
Myroides phaeus	strain=DSM 23313	GCA_900099675.1	702745	702745	type	True	78.592	199	981	95	below_threshold
Myroides fluvii	strain=CJ210	GCA_009792295.1	2572594	2572594	type	True	78.5682	197	981	95	below_threshold
Myroides injenensis	strain=M09-0166	GCA_000246945.2	1183151	1183151	type	True	78.3203	211	981	95	below_threshold
Flavobacterium inviolabile	strain=P2-65	GCA_013389455.1	2748320	2748320	type	True	77.6864	97	981	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	77.2438	91	981	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	77.2438	91	981	95	below_threshold
Flavobacterium arcticum	strain=SM1502	GCA_003344925.1	1784713	1784713	type	True	77.1737	59	981	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	77.173	83	981	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	77.1444	62	981	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	77.1313	75	981	95	below_threshold
Flavobacterium arcticum	strain=KCTC 42668	GCA_004634185.1	1784713	1784713	type	True	77.0152	62	981	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	76.8898	73	981	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	76.8545	84	981	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	76.8277	78	981	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2606	61	981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:20,611] [INFO] DFAST Taxonomy check result was written to GCF_004364575.1_ASM436457v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:20,611] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:20,612] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:20,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0575b5fd-8756-4252-b541-e367e9deace7/dqc_reference/checkm_data
[2024-01-24 13:10:20,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:20,646] [INFO] Task started: CheckM
[2024-01-24 13:10:20,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004364575.1_ASM436457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004364575.1_ASM436457v1_genomic.fna/checkm_input GCF_004364575.1_ASM436457v1_genomic.fna/checkm_result
[2024-01-24 13:10:55,849] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:55,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:55,869] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:55,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:55,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004364575.1_ASM436457v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:55,871] [INFO] Task started: Blastn
[2024-01-24 13:10:55,871] [INFO] Running command: blastn -query GCF_004364575.1_ASM436457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0575b5fd-8756-4252-b541-e367e9deace7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004364575.1_ASM436457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:56,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:56,775] [INFO] Selected 22 target genomes.
[2024-01-24 13:10:56,775] [INFO] Target genome list was writen to GCF_004364575.1_ASM436457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:56,809] [INFO] Task started: fastANI
[2024-01-24 13:10:56,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ac6966a-6158-4564-9352-19a5a50d15ae/GCF_004364575.1_ASM436457v1_genomic.fna.gz --refList GCF_004364575.1_ASM436457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004364575.1_ASM436457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:09,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:09,228] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:09,229] [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_004364575.1	s__Flavobacterium indicum_A	100.0	979	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.67	95.67	0.82	0.82	2	conclusive
GCF_001485415.1	s__Flavobacterium odoratimimum	79.42	173	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.35	97.00	0.91	0.88	14	-
GCF_000833025.1	s__Flavobacterium profundi	79.3194	173	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009711045.1	s__Flavobacterium album_A	79.2174	191	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.30	99.30	0.90	0.90	2	-
GCF_001549985.1	s__Flavobacterium odoratum_A	78.9049	225	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145665.1	s__Flavobacterium sp014145665	78.8872	186	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243275.1	s__Flavobacterium odoratum	78.7324	229	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.25	95.68	0.94	0.87	6	-
GCF_900109075.1	s__Flavobacterium marinum_A	78.6727	178	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.56	0.90	0.90	4	-
GCF_900099675.1	s__Flavobacterium phaeum	78.5933	200	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799805.1	s__Flavobacterium phaeum_A	78.5854	218	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009792295.1	s__Flavobacterium sp009792295	78.5404	196	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246945.1	s__Flavobacterium injenense	78.3293	212	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151275.1	s__Flavobacterium sp004151275	78.0094	119	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114085.1	s__Flavobacterium guanonis	77.9385	145	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	77.2382	90	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002217245.1	s__Flavobacterium columnare_A	77.1904	77	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.08	98.79	0.92	0.89	11	-
GCF_004363695.1	s__Flavobacterium cheniae	77.1351	82	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003344925.1	s__Flavobacterium arcticum	77.1276	60	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259835.1	s__Flavobacterium aquaticum	77.1244	73	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	76.7568	79	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129795.1	s__Flavobacterium sp900129795	76.5165	89	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:09,230] [INFO] GTDB search result was written to GCF_004364575.1_ASM436457v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:09,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:09,244] [INFO] DFAST_QC result json was written to GCF_004364575.1_ASM436457v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:09,244] [INFO] DFAST_QC completed!
[2024-01-24 13:11:09,244] [INFO] Total running time: 0h1m18s