[2024-01-24 14:04:44,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:04:44,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:04:44,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg71913aae-2d0f-4103-bea7-f5303f28e028/dqc_reference
[2024-01-24 14:04:45,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:04:45,521] [INFO] Task started: Prodigal
[2024-01-24 14:04:45,521] [INFO] Running command: gunzip -c /var/lib/cwl/stgc44fc84a-136e-4d92-9c08-7f60dbcfa36f/GCF_002023205.1_ASM202320v1_genomic.fna.gz | prodigal -d GCF_002023205.1_ASM202320v1_genomic.fna/cds.fna -a GCF_002023205.1_ASM202320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:00,391] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:00,391] [INFO] Task started: HMMsearch
[2024-01-24 14:05:00,392] [INFO] Running command: hmmsearch --tblout GCF_002023205.1_ASM202320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71913aae-2d0f-4103-bea7-f5303f28e028/dqc_reference/reference_markers.hmm GCF_002023205.1_ASM202320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:00,664] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:00,666] [INFO] Found 6/6 markers.
[2024-01-24 14:05:00,715] [INFO] Query marker FASTA was written to GCF_002023205.1_ASM202320v1_genomic.fna/markers.fasta
[2024-01-24 14:05:00,716] [INFO] Task started: Blastn
[2024-01-24 14:05:00,716] [INFO] Running command: blastn -query GCF_002023205.1_ASM202320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71913aae-2d0f-4103-bea7-f5303f28e028/dqc_reference/reference_markers.fasta -out GCF_002023205.1_ASM202320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:01,364] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:01,368] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:01,369] [INFO] Target genome list was writen to GCF_002023205.1_ASM202320v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:01,399] [INFO] Task started: fastANI
[2024-01-24 14:05:01,399] [INFO] Running command: fastANI --query /var/lib/cwl/stgc44fc84a-136e-4d92-9c08-7f60dbcfa36f/GCF_002023205.1_ASM202320v1_genomic.fna.gz --refList GCF_002023205.1_ASM202320v1_genomic.fna/target_genomes.txt --output GCF_002023205.1_ASM202320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:12,306] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:12,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71913aae-2d0f-4103-bea7-f5303f28e028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:12,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71913aae-2d0f-4103-bea7-f5303f28e028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:12,320] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:05:12,320] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:12,321] [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
Elizabethkingia bruuniana	strain=G0146	GCA_002023205.1	1756149	1756149	type	True	100.0	1451	1451	95	conclusive
Elizabethkingia bruuniana	strain=G0146	GCA_002024805.1	1756149	1756149	type	True	99.9999	1451	1451	95	conclusive
Elizabethkingia miricola	strain=DSM 14571	GCA_008124555.1	172045	172045	type	True	93.7846	1228	1451	95	below_threshold
Elizabethkingia miricola	strain=GTC_862	GCA_001675285.1	172045	172045	type	True	93.6712	1229	1451	95	below_threshold
Elizabethkingia anophelis		GCA_017124975.1	1117645	1117645	type	True	91.7597	1129	1451	95	below_threshold
Elizabethkingia anophelis	strain=R26	GCA_002023665.2	1117645	1117645	type	True	91.7462	1151	1451	95	below_threshold
Elizabethkingia anophelis	strain=R26	GCA_000331815.1	1117645	1117645	type	True	91.7256	1139	1451	95	below_threshold
Elizabethkingia ursingii	strain=G4122	GCA_001521765.1	1756150	1756150	type	True	91.4901	1209	1451	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.5374	83	1451	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.5367	83	1451	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	77.3855	184	1451	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	76.5543	107	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:12,322] [INFO] DFAST Taxonomy check result was written to GCF_002023205.1_ASM202320v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:12,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:12,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:12,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71913aae-2d0f-4103-bea7-f5303f28e028/dqc_reference/checkm_data
[2024-01-24 14:05:12,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:12,364] [INFO] Task started: CheckM
[2024-01-24 14:05:12,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002023205.1_ASM202320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002023205.1_ASM202320v1_genomic.fna/checkm_input GCF_002023205.1_ASM202320v1_genomic.fna/checkm_result
[2024-01-24 14:05:57,489] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:57,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:57,510] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:57,510] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:57,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002023205.1_ASM202320v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:57,511] [INFO] Task started: Blastn
[2024-01-24 14:05:57,511] [INFO] Running command: blastn -query GCF_002023205.1_ASM202320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71913aae-2d0f-4103-bea7-f5303f28e028/dqc_reference/reference_markers_gtdb.fasta -out GCF_002023205.1_ASM202320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:58,389] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:58,392] [INFO] Selected 6 target genomes.
[2024-01-24 14:05:58,392] [INFO] Target genome list was writen to GCF_002023205.1_ASM202320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:58,417] [INFO] Task started: fastANI
[2024-01-24 14:05:58,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgc44fc84a-136e-4d92-9c08-7f60dbcfa36f/GCF_002023205.1_ASM202320v1_genomic.fna.gz --refList GCF_002023205.1_ASM202320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002023205.1_ASM202320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:04,868] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:04,875] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:04,875] [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_002024805.1	s__Elizabethkingia bruuniana	99.9999	1451	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.72	96.90	0.94	0.86	13	conclusive
GCF_001675285.1	s__Elizabethkingia miricola	93.6712	1229	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.66	96.19	0.91	0.86	23	-
GCF_002023665.2	s__Elizabethkingia anophelis	91.7312	1152	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.27	97.37	0.90	0.86	104	-
GCF_001521765.1	s__Elizabethkingia ursingii	91.4843	1209	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.28	97.02	0.89	0.88	5	-
GCF_002023715.1	s__Elizabethkingia occulta	91.2051	1151	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	99.55	99.55	0.94	0.94	2	-
GCF_003058195.1	s__Elizabethkingia sp003058195	91.0875	1172	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:04,877] [INFO] GTDB search result was written to GCF_002023205.1_ASM202320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:04,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:04,880] [INFO] DFAST_QC result json was written to GCF_002023205.1_ASM202320v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:04,880] [INFO] DFAST_QC completed!
[2024-01-24 14:06:04,881] [INFO] Total running time: 0h1m21s