[2024-01-24 13:55:19,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b1016c3-e9ba-41dd-8d5d-393f02ea44fc/dqc_reference
[2024-01-24 13:55:21,146] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,146] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,147] [INFO] Running command: gunzip -c /var/lib/cwl/stgae1a45ad-472a-4d9a-b689-928aa883d36f/GCF_017124975.1_PDT000949480.1_genomic.fna.gz | prodigal -d GCF_017124975.1_PDT000949480.1_genomic.fna/cds.fna -a GCF_017124975.1_PDT000949480.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:35,376] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:35,376] [INFO] Task started: HMMsearch
[2024-01-24 13:55:35,376] [INFO] Running command: hmmsearch --tblout GCF_017124975.1_PDT000949480.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b1016c3-e9ba-41dd-8d5d-393f02ea44fc/dqc_reference/reference_markers.hmm GCF_017124975.1_PDT000949480.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:35,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:35,717] [INFO] Found 6/6 markers.
[2024-01-24 13:55:35,753] [INFO] Query marker FASTA was written to GCF_017124975.1_PDT000949480.1_genomic.fna/markers.fasta
[2024-01-24 13:55:35,753] [INFO] Task started: Blastn
[2024-01-24 13:55:35,753] [INFO] Running command: blastn -query GCF_017124975.1_PDT000949480.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b1016c3-e9ba-41dd-8d5d-393f02ea44fc/dqc_reference/reference_markers.fasta -out GCF_017124975.1_PDT000949480.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:36,377] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:36,381] [INFO] Selected 12 target genomes.
[2024-01-24 13:55:36,381] [INFO] Target genome list was writen to GCF_017124975.1_PDT000949480.1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:36,387] [INFO] Task started: fastANI
[2024-01-24 13:55:36,388] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1a45ad-472a-4d9a-b689-928aa883d36f/GCF_017124975.1_PDT000949480.1_genomic.fna.gz --refList GCF_017124975.1_PDT000949480.1_genomic.fna/target_genomes.txt --output GCF_017124975.1_PDT000949480.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:47,865] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:47,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b1016c3-e9ba-41dd-8d5d-393f02ea44fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:47,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b1016c3-e9ba-41dd-8d5d-393f02ea44fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:47,877] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:55:47,878] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:47,878] [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 anophelis		GCA_017124975.1	1117645	1117645	type	True	100.0	1347	1372	95	conclusive
Elizabethkingia anophelis	strain=R26	GCA_002023665.2	1117645	1117645	type	True	99.9998	1315	1372	95	conclusive
Elizabethkingia anophelis	strain=R26	GCA_000331815.1	1117645	1117645	type	True	99.9739	1303	1372	95	conclusive
Elizabethkingia miricola	strain=DSM 14571	GCA_008124555.1	172045	172045	type	True	92.201	1141	1372	95	below_threshold
Elizabethkingia miricola	strain=GTC_862	GCA_001675285.1	172045	172045	type	True	92.1751	1147	1372	95	below_threshold
Elizabethkingia bruuniana	strain=G0146	GCA_002024805.1	1756149	1756149	type	True	91.7897	1137	1372	95	below_threshold
Elizabethkingia bruuniana	strain=G0146	GCA_002023205.1	1756149	1756149	type	True	91.7865	1132	1372	95	below_threshold
Elizabethkingia occulta	strain=G4070	GCA_002023715.1	1867263	1867263	type	True	90.5464	1116	1372	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	77.2882	174	1372	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	76.9416	168	1372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:47,880] [INFO] DFAST Taxonomy check result was written to GCF_017124975.1_PDT000949480.1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:47,882] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:47,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:47,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b1016c3-e9ba-41dd-8d5d-393f02ea44fc/dqc_reference/checkm_data
[2024-01-24 13:55:47,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:47,932] [INFO] Task started: CheckM
[2024-01-24 13:55:47,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017124975.1_PDT000949480.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017124975.1_PDT000949480.1_genomic.fna/checkm_input GCF_017124975.1_PDT000949480.1_genomic.fna/checkm_result
[2024-01-24 13:56:32,410] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:32,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:32,438] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:32,438] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:32,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017124975.1_PDT000949480.1_genomic.fna/markers.fasta)
[2024-01-24 13:56:32,440] [INFO] Task started: Blastn
[2024-01-24 13:56:32,440] [INFO] Running command: blastn -query GCF_017124975.1_PDT000949480.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b1016c3-e9ba-41dd-8d5d-393f02ea44fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_017124975.1_PDT000949480.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:33,298] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:33,302] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:33,303] [INFO] Target genome list was writen to GCF_017124975.1_PDT000949480.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:33,316] [INFO] Task started: fastANI
[2024-01-24 13:56:33,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1a45ad-472a-4d9a-b689-928aa883d36f/GCF_017124975.1_PDT000949480.1_genomic.fna.gz --refList GCF_017124975.1_PDT000949480.1_genomic.fna/target_genomes_gtdb.txt --output GCF_017124975.1_PDT000949480.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:41,983] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:41,995] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:41,995] [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_002023665.2	s__Elizabethkingia anophelis	99.9998	1315	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.27	97.37	0.90	0.86	104	conclusive
GCF_001675285.1	s__Elizabethkingia miricola	92.1752	1147	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.66	96.19	0.91	0.86	23	-
GCF_002024805.1	s__Elizabethkingia bruuniana	91.7769	1138	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.72	96.90	0.94	0.86	13	-
GCF_002023715.1	s__Elizabethkingia occulta	90.534	1117	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	99.55	99.55	0.94	0.94	2	-
GCF_001521765.1	s__Elizabethkingia ursingii	89.8847	1124	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.28	97.02	0.89	0.88	5	-
GCF_003058195.1	s__Elizabethkingia sp003058195	89.6533	1077	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900101995.1	s__Riemerella columbipharyngis	77.03	63	1372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Riemerella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:41,996] [INFO] GTDB search result was written to GCF_017124975.1_PDT000949480.1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:41,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:42,000] [INFO] DFAST_QC result json was written to GCF_017124975.1_PDT000949480.1_genomic.fna/dqc_result.json
[2024-01-24 13:56:42,001] [INFO] DFAST_QC completed!
[2024-01-24 13:56:42,001] [INFO] Total running time: 0h1m22s