[2024-01-24 11:34:53,507] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:53,509] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:53,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgc07c606e-11d6-473c-a57a-ce7b10e5394a/dqc_reference
[2024-01-24 11:34:55,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:55,646] [INFO] Task started: Prodigal
[2024-01-24 11:34:55,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg36813284-d2a0-4088-bdef-68d9a2f5b817/GCF_007474545.1_ASM747454v1_genomic.fna.gz | prodigal -d GCF_007474545.1_ASM747454v1_genomic.fna/cds.fna -a GCF_007474545.1_ASM747454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:08,697] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:08,697] [INFO] Task started: HMMsearch
[2024-01-24 11:35:08,697] [INFO] Running command: hmmsearch --tblout GCF_007474545.1_ASM747454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc07c606e-11d6-473c-a57a-ce7b10e5394a/dqc_reference/reference_markers.hmm GCF_007474545.1_ASM747454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:08,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:08,983] [INFO] Found 6/6 markers.
[2024-01-24 11:35:09,018] [INFO] Query marker FASTA was written to GCF_007474545.1_ASM747454v1_genomic.fna/markers.fasta
[2024-01-24 11:35:09,018] [INFO] Task started: Blastn
[2024-01-24 11:35:09,019] [INFO] Running command: blastn -query GCF_007474545.1_ASM747454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc07c606e-11d6-473c-a57a-ce7b10e5394a/dqc_reference/reference_markers.fasta -out GCF_007474545.1_ASM747454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:09,686] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:09,690] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:09,691] [INFO] Target genome list was writen to GCF_007474545.1_ASM747454v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:09,701] [INFO] Task started: fastANI
[2024-01-24 11:35:09,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg36813284-d2a0-4088-bdef-68d9a2f5b817/GCF_007474545.1_ASM747454v1_genomic.fna.gz --refList GCF_007474545.1_ASM747454v1_genomic.fna/target_genomes.txt --output GCF_007474545.1_ASM747454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:24,428] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:24,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc07c606e-11d6-473c-a57a-ce7b10e5394a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:24,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc07c606e-11d6-473c-a57a-ce7b10e5394a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:24,443] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:24,443] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:24,443] [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 binzhouense	strain=LM2	GCA_007474545.1	2593646	2593646	type	True	100.0	1196	1197	95	conclusive
Chryseobacterium taihuense	strain=CGMCC 1.10941	GCA_900103755.1	1141221	1141221	type	True	91.6182	979	1197	95	below_threshold
Chryseobacterium echinoideorum	strain=CC-CZW010	GCA_007474535.1	1549648	1549648	type	True	88.2753	932	1197	95	below_threshold
Chryseobacterium aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	81.9782	688	1197	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	81.2157	700	1197	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	81.1975	680	1197	95	below_threshold
Chryseobacterium balustinum	strain=DSM 16775	GCA_900168205.1	246	246	type	True	80.6964	658	1197	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.5497	638	1197	95	below_threshold
Chryseobacterium taichungense	strain=DSM 17453	GCA_900109935.1	295069	295069	type	True	80.3341	543	1197	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	79.8947	535	1197	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.7616	564	1197	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.6378	569	1197	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_900156685.1	551459	551459	type	True	79.2663	494	1197	95	below_threshold
Chryseobacterium populi	strain=CF314	GCA_000282115.1	1144316	1144316	type	True	79.188	487	1197	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	79.1131	462	1197	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	76.8618	172	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:24,445] [INFO] DFAST Taxonomy check result was written to GCF_007474545.1_ASM747454v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:24,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:24,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:24,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc07c606e-11d6-473c-a57a-ce7b10e5394a/dqc_reference/checkm_data
[2024-01-24 11:35:24,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:24,483] [INFO] Task started: CheckM
[2024-01-24 11:35:24,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007474545.1_ASM747454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007474545.1_ASM747454v1_genomic.fna/checkm_input GCF_007474545.1_ASM747454v1_genomic.fna/checkm_result
[2024-01-24 11:36:06,565] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:06,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:06,585] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:06,585] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:06,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007474545.1_ASM747454v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:06,586] [INFO] Task started: Blastn
[2024-01-24 11:36:06,586] [INFO] Running command: blastn -query GCF_007474545.1_ASM747454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc07c606e-11d6-473c-a57a-ce7b10e5394a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007474545.1_ASM747454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:07,447] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:07,451] [INFO] Selected 12 target genomes.
[2024-01-24 11:36:07,452] [INFO] Target genome list was writen to GCF_007474545.1_ASM747454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:07,464] [INFO] Task started: fastANI
[2024-01-24 11:36:07,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg36813284-d2a0-4088-bdef-68d9a2f5b817/GCF_007474545.1_ASM747454v1_genomic.fna.gz --refList GCF_007474545.1_ASM747454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007474545.1_ASM747454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:17,697] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:17,713] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:17,713] [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_007474545.1	s__Chryseobacterium binzhouense	100.0	1196	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.18	97.18	0.83	0.83	2	conclusive
GCF_900103755.1	s__Chryseobacterium taihuense	91.6171	980	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.40	97.39	0.91	0.91	3	-
GCF_007474535.1	s__Chryseobacterium echinoideorum	88.278	932	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420285.1	s__Chryseobacterium aquaticum	81.9665	688	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	96.87	96.87	0.89	0.89	2	-
GCF_012952015.1	s__Chryseobacterium aquaticum_A	81.955	704	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.4843	100.00	100.00	1.00	1.00	2	-
GCF_017808115.1	s__Chryseobacterium sp017808115	81.6102	617	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006175945.1	s__Chryseobacterium mulctrae	81.2157	700	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116415.1	s__Chryseobacterium formosense	81.1978	680	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.74	97.50	0.90	0.80	3	-
GCF_000799515.1	s__Chryseobacterium sp000799515	81.085	660	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779605.1	s__Chryseobacterium sp014779605	80.9277	660	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.70	96.70	0.87	0.87	2	-
GCF_900109935.1	s__Chryseobacterium taichungense	80.3342	543	1197	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613715.1	s__Chryseobacterium sp018613715	78.8188	436	1197	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 11:36:17,715] [INFO] GTDB search result was written to GCF_007474545.1_ASM747454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:17,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:17,720] [INFO] DFAST_QC result json was written to GCF_007474545.1_ASM747454v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:17,720] [INFO] DFAST_QC completed!
[2024-01-24 11:36:17,720] [INFO] Total running time: 0h1m24s