[2024-01-24 10:57:39,019] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:39,022] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:39,024] [INFO] DQC Reference Directory: /var/lib/cwl/stgdabd095f-4887-4f69-9c03-1d63123a893c/dqc_reference
[2024-01-24 10:57:40,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,367] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,367] [INFO] Running command: gunzip -c /var/lib/cwl/stg328e45c2-d413-4bad-b465-d127b24a92a3/GCF_007474535.1_ASM747453v1_genomic.fna.gz | prodigal -d GCF_007474535.1_ASM747453v1_genomic.fna/cds.fna -a GCF_007474535.1_ASM747453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:54,280] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:54,280] [INFO] Task started: HMMsearch
[2024-01-24 10:57:54,280] [INFO] Running command: hmmsearch --tblout GCF_007474535.1_ASM747453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdabd095f-4887-4f69-9c03-1d63123a893c/dqc_reference/reference_markers.hmm GCF_007474535.1_ASM747453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:54,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:54,546] [INFO] Found 6/6 markers.
[2024-01-24 10:57:54,583] [INFO] Query marker FASTA was written to GCF_007474535.1_ASM747453v1_genomic.fna/markers.fasta
[2024-01-24 10:57:54,583] [INFO] Task started: Blastn
[2024-01-24 10:57:54,583] [INFO] Running command: blastn -query GCF_007474535.1_ASM747453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdabd095f-4887-4f69-9c03-1d63123a893c/dqc_reference/reference_markers.fasta -out GCF_007474535.1_ASM747453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:55,224] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:55,228] [INFO] Selected 18 target genomes.
[2024-01-24 10:57:55,228] [INFO] Target genome list was writen to GCF_007474535.1_ASM747453v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:55,248] [INFO] Task started: fastANI
[2024-01-24 10:57:55,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg328e45c2-d413-4bad-b465-d127b24a92a3/GCF_007474535.1_ASM747453v1_genomic.fna.gz --refList GCF_007474535.1_ASM747453v1_genomic.fna/target_genomes.txt --output GCF_007474535.1_ASM747453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:10,769] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:10,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdabd095f-4887-4f69-9c03-1d63123a893c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:10,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdabd095f-4887-4f69-9c03-1d63123a893c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:10,784] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:10,784] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:10,784] [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 echinoideorum	strain=CC-CZW010	GCA_007474535.1	1549648	1549648	type	True	100.0	1254	1255	95	conclusive
Chryseobacterium binzhouense	strain=LM2	GCA_007474545.1	2593646	2593646	type	True	88.3259	928	1255	95	below_threshold
Chryseobacterium taihuense	strain=CGMCC 1.10941	GCA_900103755.1	1141221	1141221	type	True	87.9736	906	1255	95	below_threshold
Chryseobacterium aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	81.1913	683	1255	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	80.8368	687	1255	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	80.7946	678	1255	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.5546	649	1255	95	below_threshold
Chryseobacterium balustinum	strain=DSM 16775	GCA_900168205.1	246	246	type	True	80.5211	656	1255	95	below_threshold
Chryseobacterium arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	80.2583	568	1255	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	79.9045	526	1255	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.7901	541	1255	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.7609	565	1255	95	below_threshold
Chryseobacterium populi	strain=CF314	GCA_000282115.1	1144316	1144316	type	True	79.0508	510	1255	95	below_threshold
Chryseobacterium phosphatilyticum	strain=ISE14	GCA_002899825.2	475075	475075	type	True	78.8189	455	1255	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.6559	388	1255	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	78.653	461	1255	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	78.6516	460	1255	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	76.7749	161	1255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:10,786] [INFO] DFAST Taxonomy check result was written to GCF_007474535.1_ASM747453v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:10,786] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:10,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:10,787] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdabd095f-4887-4f69-9c03-1d63123a893c/dqc_reference/checkm_data
[2024-01-24 10:58:10,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:10,825] [INFO] Task started: CheckM
[2024-01-24 10:58:10,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007474535.1_ASM747453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007474535.1_ASM747453v1_genomic.fna/checkm_input GCF_007474535.1_ASM747453v1_genomic.fna/checkm_result
[2024-01-24 10:58:54,822] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:54,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:54,847] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:54,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:54,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007474535.1_ASM747453v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:54,848] [INFO] Task started: Blastn
[2024-01-24 10:58:54,848] [INFO] Running command: blastn -query GCF_007474535.1_ASM747453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdabd095f-4887-4f69-9c03-1d63123a893c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007474535.1_ASM747453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:55,759] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:55,763] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:55,764] [INFO] Target genome list was writen to GCF_007474535.1_ASM747453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:55,773] [INFO] Task started: fastANI
[2024-01-24 10:58:55,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg328e45c2-d413-4bad-b465-d127b24a92a3/GCF_007474535.1_ASM747453v1_genomic.fna.gz --refList GCF_007474535.1_ASM747453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007474535.1_ASM747453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:07,053] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:07,065] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:07,066] [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_007474535.1	s__Chryseobacterium echinoideorum	100.0	1254	1255	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_007474545.1	s__Chryseobacterium binzhouense	88.3168	929	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.18	97.18	0.83	0.83	2	-
GCF_900103755.1	s__Chryseobacterium taihuense	87.9827	905	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.40	97.39	0.91	0.91	3	-
GCF_017808115.1	s__Chryseobacterium sp017808115	81.7867	630	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507325.1	s__Chryseobacterium greenlandense	81.4128	683	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	N/A	N/A	N/A	N/A	1	-
GCF_001420285.1	s__Chryseobacterium aquaticum	81.1974	682	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	96.87	96.87	0.89	0.89	2	-
GCF_006175945.1	s__Chryseobacterium mulctrae	80.822	674	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143185.1	s__Chryseobacterium scophthalmum	80.8135	690	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.42	95.16	0.86	0.85	5	-
GCF_900168205.1	s__Chryseobacterium balustinum	80.5375	653	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.96	99.93	0.98	0.95	3	-
GCF_001677955.1	s__Chryseobacterium sp001677955	80.3178	647	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000813825.1	s__Chryseobacterium taiwanense	79.7483	543	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282115.1	s__Chryseobacterium populi	79.0641	508	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_003385455.1	s__Chryseobacterium rhizosphaerae	78.6621	460	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.95	95.13	0.92	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:07,067] [INFO] GTDB search result was written to GCF_007474535.1_ASM747453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:07,068] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:07,072] [INFO] DFAST_QC result json was written to GCF_007474535.1_ASM747453v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:07,072] [INFO] DFAST_QC completed!
[2024-01-24 10:59:07,072] [INFO] Total running time: 0h1m28s