[2024-01-24 10:48:09,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,229] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,229] [INFO] DQC Reference Directory: /var/lib/cwl/stgf72a17aa-fe1d-471d-ae82-0603e429dc22/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,959] [INFO] Running command: gunzip -c /var/lib/cwl/stgffa7ee35-4310-4dc6-9926-711ac34c0eb1/GCF_003385515.1_ASM338551v1_genomic.fna.gz | prodigal -d GCF_003385515.1_ASM338551v1_genomic.fna/cds.fna -a GCF_003385515.1_ASM338551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:45,639] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:45,640] [INFO] Task started: HMMsearch
[2024-01-24 10:48:45,640] [INFO] Running command: hmmsearch --tblout GCF_003385515.1_ASM338551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf72a17aa-fe1d-471d-ae82-0603e429dc22/dqc_reference/reference_markers.hmm GCF_003385515.1_ASM338551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:45,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:45,975] [INFO] Found 6/6 markers.
[2024-01-24 10:48:46,022] [INFO] Query marker FASTA was written to GCF_003385515.1_ASM338551v1_genomic.fna/markers.fasta
[2024-01-24 10:48:46,023] [INFO] Task started: Blastn
[2024-01-24 10:48:46,023] [INFO] Running command: blastn -query GCF_003385515.1_ASM338551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf72a17aa-fe1d-471d-ae82-0603e429dc22/dqc_reference/reference_markers.fasta -out GCF_003385515.1_ASM338551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:46,713] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:46,717] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:46,717] [INFO] Target genome list was writen to GCF_003385515.1_ASM338551v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:46,725] [INFO] Task started: fastANI
[2024-01-24 10:48:46,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgffa7ee35-4310-4dc6-9926-711ac34c0eb1/GCF_003385515.1_ASM338551v1_genomic.fna.gz --refList GCF_003385515.1_ASM338551v1_genomic.fna/target_genomes.txt --output GCF_003385515.1_ASM338551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:03,091] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:03,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf72a17aa-fe1d-471d-ae82-0603e429dc22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:03,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf72a17aa-fe1d-471d-ae82-0603e429dc22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:03,109] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:49:03,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:03,109] [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
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	100.0	2023	2024	95	conclusive
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	87.1525	1348	2024	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	86.7282	1373	2024	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	86.2545	1290	2024	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	84.353	1195	2024	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	84.3034	1173	2024	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	84.1213	1149	2024	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	84.1028	1132	2024	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	83.3573	1086	2024	95	below_threshold
Chryseobacterium lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	82.8904	1158	2024	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.4397	677	2024	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.8556	747	2024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:03,111] [INFO] DFAST Taxonomy check result was written to GCF_003385515.1_ASM338551v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:03,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:03,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:03,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf72a17aa-fe1d-471d-ae82-0603e429dc22/dqc_reference/checkm_data
[2024-01-24 10:49:03,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:03,225] [INFO] Task started: CheckM
[2024-01-24 10:49:03,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385515.1_ASM338551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385515.1_ASM338551v1_genomic.fna/checkm_input GCF_003385515.1_ASM338551v1_genomic.fna/checkm_result
[2024-01-24 10:50:11,338] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:11,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:11,368] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:11,368] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:11,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385515.1_ASM338551v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:11,369] [INFO] Task started: Blastn
[2024-01-24 10:50:11,369] [INFO] Running command: blastn -query GCF_003385515.1_ASM338551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf72a17aa-fe1d-471d-ae82-0603e429dc22/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385515.1_ASM338551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:12,323] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:12,327] [INFO] Selected 13 target genomes.
[2024-01-24 10:50:12,328] [INFO] Target genome list was writen to GCF_003385515.1_ASM338551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:12,360] [INFO] Task started: fastANI
[2024-01-24 10:50:12,361] [INFO] Running command: fastANI --query /var/lib/cwl/stgffa7ee35-4310-4dc6-9926-711ac34c0eb1/GCF_003385515.1_ASM338551v1_genomic.fna.gz --refList GCF_003385515.1_ASM338551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385515.1_ASM338551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:30,001] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:30,022] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:30,022] [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_003385515.1	s__Chryseobacterium sp003385515	100.0	2023	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	conclusive
GCF_003815715.1	s__Chryseobacterium sp003815715	87.1642	1355	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637665.1	s__Chryseobacterium nakagawai	87.1356	1350	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	86.9898	1374	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078205.2	s__Chryseobacterium timonianum	86.8901	1389	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100075.1	s__Chryseobacterium jejuense	86.7457	1370	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000829375.1	s__Chryseobacterium sp000829375	86.5527	1373	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119455.1	s__Chryseobacterium sp004119455	86.5521	1302	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009900745.1	s__Chryseobacterium sp009900745	86.3236	1365	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218825.1	s__Chryseobacterium bernardetii	86.2488	1307	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.97	99.97	0.99	0.99	3	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	84.366	1193	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	83.2292	1090	2024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_003058195.1	s__Elizabethkingia sp003058195	77.5533	242	2024	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 10:50:30,024] [INFO] GTDB search result was written to GCF_003385515.1_ASM338551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:30,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:30,028] [INFO] DFAST_QC result json was written to GCF_003385515.1_ASM338551v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:30,028] [INFO] DFAST_QC completed!
[2024-01-24 10:50:30,028] [INFO] Total running time: 0h2m21s