[2024-01-24 12:52:23,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:23,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:23,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg615fbd07-b4aa-4f85-983c-45d9a617c238/dqc_reference
[2024-01-24 12:52:24,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:24,695] [INFO] Task started: Prodigal
[2024-01-24 12:52:24,695] [INFO] Running command: gunzip -c /var/lib/cwl/stgf429ccd2-e51e-4568-8c28-96eb7ab9464d/GCF_003634775.1_ASM363477v1_genomic.fna.gz | prodigal -d GCF_003634775.1_ASM363477v1_genomic.fna/cds.fna -a GCF_003634775.1_ASM363477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:39,021] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:39,022] [INFO] Task started: HMMsearch
[2024-01-24 12:52:39,022] [INFO] Running command: hmmsearch --tblout GCF_003634775.1_ASM363477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg615fbd07-b4aa-4f85-983c-45d9a617c238/dqc_reference/reference_markers.hmm GCF_003634775.1_ASM363477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:39,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:39,295] [INFO] Found 6/6 markers.
[2024-01-24 12:52:39,326] [INFO] Query marker FASTA was written to GCF_003634775.1_ASM363477v1_genomic.fna/markers.fasta
[2024-01-24 12:52:39,327] [INFO] Task started: Blastn
[2024-01-24 12:52:39,327] [INFO] Running command: blastn -query GCF_003634775.1_ASM363477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg615fbd07-b4aa-4f85-983c-45d9a617c238/dqc_reference/reference_markers.fasta -out GCF_003634775.1_ASM363477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:39,993] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:39,997] [INFO] Selected 18 target genomes.
[2024-01-24 12:52:39,997] [INFO] Target genome list was writen to GCF_003634775.1_ASM363477v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:40,037] [INFO] Task started: fastANI
[2024-01-24 12:52:40,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgf429ccd2-e51e-4568-8c28-96eb7ab9464d/GCF_003634775.1_ASM363477v1_genomic.fna.gz --refList GCF_003634775.1_ASM363477v1_genomic.fna/target_genomes.txt --output GCF_003634775.1_ASM363477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:56,983] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:56,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg615fbd07-b4aa-4f85-983c-45d9a617c238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:56,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg615fbd07-b4aa-4f85-983c-45d9a617c238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:57,001] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:52:57,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:57,002] [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 defluvii	strain=DSM 14219	GCA_003634775.1	160396	160396	type	True	100.0	1233	1233	95	conclusive
Chryseobacterium daecheongense	strain=DSM 15235	GCA_004365465.1	192389	192389	type	True	86.4935	1013	1233	95	below_threshold
Chryseobacterium daecheongense	strain=DSM 15235	GCA_003729955.1	192389	192389	type	True	86.4597	1014	1233	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.4741	665	1233	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	80.4568	709	1233	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.3279	673	1233	95	below_threshold
Chryseobacterium vaccae	strain=CA7	GCA_009602705.1	2604424	2604424	type	True	80.3168	687	1233	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	80.2742	678	1233	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	80.27	698	1233	95	below_threshold
Chryseobacterium piperi	strain=ATCC BAA-1782	GCA_002285635.2	558152	558152	type	True	80.2503	629	1233	95	below_threshold
Chryseobacterium piperi	strain=CTM	GCA_000737775.1	558152	558152	type	True	80.2373	627	1233	95	below_threshold
Chryseobacterium culicis	strain=DSM 23031	GCA_900108365.1	680127	680127	type	True	80.1773	696	1233	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.0905	721	1233	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	80.0732	698	1233	95	below_threshold
Chryseobacterium phocaeense	strain=6021061333	GCA_900169075.1	1816690	1816690	type	True	79.8018	696	1233	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	79.7945	607	1233	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.2503	477	1233	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.1553	548	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:57,004] [INFO] DFAST Taxonomy check result was written to GCF_003634775.1_ASM363477v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:57,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:57,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:57,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg615fbd07-b4aa-4f85-983c-45d9a617c238/dqc_reference/checkm_data
[2024-01-24 12:52:57,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:57,044] [INFO] Task started: CheckM
[2024-01-24 12:52:57,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634775.1_ASM363477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634775.1_ASM363477v1_genomic.fna/checkm_input GCF_003634775.1_ASM363477v1_genomic.fna/checkm_result
[2024-01-24 12:53:40,995] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:40,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:41,017] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:41,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:41,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634775.1_ASM363477v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:41,018] [INFO] Task started: Blastn
[2024-01-24 12:53:41,018] [INFO] Running command: blastn -query GCF_003634775.1_ASM363477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg615fbd07-b4aa-4f85-983c-45d9a617c238/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634775.1_ASM363477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:41,936] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:41,941] [INFO] Selected 21 target genomes.
[2024-01-24 12:53:41,941] [INFO] Target genome list was writen to GCF_003634775.1_ASM363477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:41,975] [INFO] Task started: fastANI
[2024-01-24 12:53:41,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgf429ccd2-e51e-4568-8c28-96eb7ab9464d/GCF_003634775.1_ASM363477v1_genomic.fna.gz --refList GCF_003634775.1_ASM363477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634775.1_ASM363477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:01,009] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:01,032] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:01,032] [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_003634775.1	s__Chryseobacterium defluvii	100.0	1233	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003729955.1	s__Chryseobacterium daecheongense	86.4752	1012	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014204415.1	s__Chryseobacterium defluvii_A	81.404	721	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593385.1	s__Chryseobacterium cucumeris	80.5071	709	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.67	98.29	0.93	0.90	5	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	80.4679	707	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_001295265.1	s__Chryseobacterium indologenes_A	80.3734	684	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813825.1	s__Chryseobacterium taiwanense	80.3668	671	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799235.1	s__Chryseobacterium sp000799235	80.3243	714	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009602705.1	s__Chryseobacterium vaccae	80.3228	687	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274625.1	s__Chryseobacterium sp008274625	80.3058	693	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285635.2	s__Chryseobacterium piperi	80.2505	629	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000799455.1	s__Chryseobacterium sp000799455	80.2207	677	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410675.1	s__Chryseobacterium sp013410675	80.1925	685	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108365.1	s__Chryseobacterium culicis	80.1608	698	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.67	98.65	0.92	0.91	3	-
GCF_000799335.1	s__Chryseobacterium sp000799335	80.1385	710	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002025665.1	s__Chryseobacterium indologenes_F	80.1288	721	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815715.1	s__Chryseobacterium sp003815715	80.1084	666	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045465.1	s__Chryseobacterium angstadtii	80.0711	696	1233	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	79.9905	660	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016745235.1	s__Chryseobacterium sp016745235	79.9751	710	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169075.1	s__Chryseobacterium phocaeense	79.7981	696	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:01,035] [INFO] GTDB search result was written to GCF_003634775.1_ASM363477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:01,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:01,040] [INFO] DFAST_QC result json was written to GCF_003634775.1_ASM363477v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:01,040] [INFO] DFAST_QC completed!
[2024-01-24 12:54:01,040] [INFO] Total running time: 0h1m38s