[2024-01-24 13:09:33,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg4209deb2-324e-4696-8988-d525963a3175/dqc_reference
[2024-01-24 13:09:35,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,102] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg27b46c08-b148-48b0-b919-b3d6be9da9c6/GCF_001521765.1_ASM152176v1_genomic.fna.gz | prodigal -d GCF_001521765.1_ASM152176v1_genomic.fna/cds.fna -a GCF_001521765.1_ASM152176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:50,408] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:50,408] [INFO] Task started: HMMsearch
[2024-01-24 13:09:50,408] [INFO] Running command: hmmsearch --tblout GCF_001521765.1_ASM152176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4209deb2-324e-4696-8988-d525963a3175/dqc_reference/reference_markers.hmm GCF_001521765.1_ASM152176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:50,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:50,677] [INFO] Found 6/6 markers.
[2024-01-24 13:09:50,713] [INFO] Query marker FASTA was written to GCF_001521765.1_ASM152176v1_genomic.fna/markers.fasta
[2024-01-24 13:09:50,714] [INFO] Task started: Blastn
[2024-01-24 13:09:50,714] [INFO] Running command: blastn -query GCF_001521765.1_ASM152176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4209deb2-324e-4696-8988-d525963a3175/dqc_reference/reference_markers.fasta -out GCF_001521765.1_ASM152176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:51,355] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:51,359] [INFO] Selected 12 target genomes.
[2024-01-24 13:09:51,359] [INFO] Target genome list was writen to GCF_001521765.1_ASM152176v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:51,366] [INFO] Task started: fastANI
[2024-01-24 13:09:51,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg27b46c08-b148-48b0-b919-b3d6be9da9c6/GCF_001521765.1_ASM152176v1_genomic.fna.gz --refList GCF_001521765.1_ASM152176v1_genomic.fna/target_genomes.txt --output GCF_001521765.1_ASM152176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:01,265] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:01,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4209deb2-324e-4696-8988-d525963a3175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:01,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4209deb2-324e-4696-8988-d525963a3175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:01,277] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:01,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:01,277] [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 ursingii	strain=G4122	GCA_001521765.1	1756150	1756150	type	True	100.0	1418	1421	95	conclusive
Elizabethkingia occulta	strain=G4070	GCA_002023715.1	1867263	1867263	type	True	94.7284	1170	1421	95	below_threshold
Elizabethkingia bruuniana	strain=G0146	GCA_002023205.1	1756149	1756149	type	True	91.4861	1201	1421	95	below_threshold
Elizabethkingia bruuniana	strain=G0146	GCA_002024805.1	1756149	1756149	type	True	91.4508	1205	1421	95	below_threshold
Elizabethkingia miricola	strain=GTC_862	GCA_001675285.1	172045	172045	type	True	91.1612	1186	1421	95	below_threshold
Elizabethkingia miricola	strain=DSM 14571	GCA_008124555.1	172045	172045	type	True	91.0934	1192	1421	95	below_threshold
Elizabethkingia anophelis	strain=R26	GCA_000331815.1	1117645	1117645	type	True	89.9291	1130	1421	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	77.2231	179	1421	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.0423	97	1421	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.0423	97	1421	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	76.7491	101	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:01,279] [INFO] DFAST Taxonomy check result was written to GCF_001521765.1_ASM152176v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:01,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:01,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:01,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4209deb2-324e-4696-8988-d525963a3175/dqc_reference/checkm_data
[2024-01-24 13:10:01,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:01,326] [INFO] Task started: CheckM
[2024-01-24 13:10:01,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001521765.1_ASM152176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001521765.1_ASM152176v1_genomic.fna/checkm_input GCF_001521765.1_ASM152176v1_genomic.fna/checkm_result
[2024-01-24 13:10:43,737] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:43,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:43,755] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:43,756] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:43,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001521765.1_ASM152176v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:43,756] [INFO] Task started: Blastn
[2024-01-24 13:10:43,756] [INFO] Running command: blastn -query GCF_001521765.1_ASM152176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4209deb2-324e-4696-8988-d525963a3175/dqc_reference/reference_markers_gtdb.fasta -out GCF_001521765.1_ASM152176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:44,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:44,583] [INFO] Selected 6 target genomes.
[2024-01-24 13:10:44,583] [INFO] Target genome list was writen to GCF_001521765.1_ASM152176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:44,588] [INFO] Task started: fastANI
[2024-01-24 13:10:44,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg27b46c08-b148-48b0-b919-b3d6be9da9c6/GCF_001521765.1_ASM152176v1_genomic.fna.gz --refList GCF_001521765.1_ASM152176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001521765.1_ASM152176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:51,128] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:51,135] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:51,135] [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_001521765.1	s__Elizabethkingia ursingii	100.0	1418	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.28	97.02	0.89	0.88	5	conclusive
GCF_002023715.1	s__Elizabethkingia occulta	94.7284	1170	1421	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	93.5965	1158	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002024805.1	s__Elizabethkingia bruuniana	91.4508	1205	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.72	96.90	0.94	0.86	13	-
GCF_001675285.1	s__Elizabethkingia miricola	91.1682	1185	1421	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	89.8769	1140	1421	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.27	97.37	0.90	0.86	104	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:51,137] [INFO] GTDB search result was written to GCF_001521765.1_ASM152176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:51,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:51,140] [INFO] DFAST_QC result json was written to GCF_001521765.1_ASM152176v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:51,140] [INFO] DFAST_QC completed!
[2024-01-24 13:10:51,140] [INFO] Total running time: 0h1m17s