[2024-01-24 13:42:57,451] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,454] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9bc3ab0-1d18-490d-ab59-cee411433129/dqc_reference
[2024-01-24 13:42:58,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,718] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg4832debf-5066-4a8c-9c14-3aaf8356e6cc/GCF_000430825.1_ASM43082v1_genomic.fna.gz | prodigal -d GCF_000430825.1_ASM43082v1_genomic.fna/cds.fna -a GCF_000430825.1_ASM43082v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:13,931] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:13,932] [INFO] Task started: HMMsearch
[2024-01-24 13:43:13,932] [INFO] Running command: hmmsearch --tblout GCF_000430825.1_ASM43082v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9bc3ab0-1d18-490d-ab59-cee411433129/dqc_reference/reference_markers.hmm GCF_000430825.1_ASM43082v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:14,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:14,241] [INFO] Found 6/6 markers.
[2024-01-24 13:43:14,278] [INFO] Query marker FASTA was written to GCF_000430825.1_ASM43082v1_genomic.fna/markers.fasta
[2024-01-24 13:43:14,278] [INFO] Task started: Blastn
[2024-01-24 13:43:14,278] [INFO] Running command: blastn -query GCF_000430825.1_ASM43082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9bc3ab0-1d18-490d-ab59-cee411433129/dqc_reference/reference_markers.fasta -out GCF_000430825.1_ASM43082v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:14,915] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:14,918] [INFO] Selected 17 target genomes.
[2024-01-24 13:43:14,918] [INFO] Target genome list was writen to GCF_000430825.1_ASM43082v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:14,929] [INFO] Task started: fastANI
[2024-01-24 13:43:14,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg4832debf-5066-4a8c-9c14-3aaf8356e6cc/GCF_000430825.1_ASM43082v1_genomic.fna.gz --refList GCF_000430825.1_ASM43082v1_genomic.fna/target_genomes.txt --output GCF_000430825.1_ASM43082v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:30,622] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:30,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9bc3ab0-1d18-490d-ab59-cee411433129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:30,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9bc3ab0-1d18-490d-ab59-cee411433129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:30,640] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:30,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:30,640] [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 daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	100.0	1382	1391	95	conclusive
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	83.6601	983	1391	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	82.3149	935	1391	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	82.1283	855	1391	95	below_threshold
Chryseobacterium arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	82.0976	873	1391	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	81.7118	710	1391	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	81.6716	815	1391	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	81.509	778	1391	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	81.4055	767	1391	95	below_threshold
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	81.0417	789	1391	95	below_threshold
Chryseobacterium carnipullorum	strain=DSM 25581	GCA_900142785.1	1124835	1124835	type	True	80.5701	677	1391	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	80.4372	731	1391	95	below_threshold
Chryseobacterium elymi	strain=KCTC 22547	GCA_003385495.1	395936	395936	type	True	80.4077	712	1391	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	80.3577	686	1391	95	below_threshold
Chryseobacterium vrystaatense	strain=LMG 22846	GCA_000737765.1	307480	307480	type	True	80.225	682	1391	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.7691	648	1391	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	76.8714	168	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:30,642] [INFO] DFAST Taxonomy check result was written to GCF_000430825.1_ASM43082v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:30,642] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:30,642] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:30,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9bc3ab0-1d18-490d-ab59-cee411433129/dqc_reference/checkm_data
[2024-01-24 13:43:30,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:30,689] [INFO] Task started: CheckM
[2024-01-24 13:43:30,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430825.1_ASM43082v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430825.1_ASM43082v1_genomic.fna/checkm_input GCF_000430825.1_ASM43082v1_genomic.fna/checkm_result
[2024-01-24 13:44:17,173] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:17,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:17,192] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:17,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:17,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430825.1_ASM43082v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:17,193] [INFO] Task started: Blastn
[2024-01-24 13:44:17,193] [INFO] Running command: blastn -query GCF_000430825.1_ASM43082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9bc3ab0-1d18-490d-ab59-cee411433129/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430825.1_ASM43082v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:18,046] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:18,050] [INFO] Selected 19 target genomes.
[2024-01-24 13:44:18,050] [INFO] Target genome list was writen to GCF_000430825.1_ASM43082v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:18,079] [INFO] Task started: fastANI
[2024-01-24 13:44:18,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg4832debf-5066-4a8c-9c14-3aaf8356e6cc/GCF_000430825.1_ASM43082v1_genomic.fna.gz --refList GCF_000430825.1_ASM43082v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430825.1_ASM43082v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:38,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:38,169] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:38,169] [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_000430825.1	s__Chryseobacterium daeguense	100.0	1380	1391	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_900111495.1	s__Chryseobacterium wanjuense	83.6529	984	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456155.1	s__Chryseobacterium sp001456155	83.6375	968	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.07	98.07	0.94	0.94	2	-
GCF_900156075.1	s__Chryseobacterium sp900156075	82.9154	753	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799195.1	s__Chryseobacterium sp000799195	82.6234	934	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156825.1	s__Chryseobacterium gambrini	82.1488	853	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_900129245.1	s__Chryseobacterium arachidis	82.098	873	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425355.1	s__Chryseobacterium sp001425355	81.8428	858	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799455.1	s__Chryseobacterium sp000799455	81.6828	773	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002177115.1	s__Chryseobacterium mucoviscidosis	81.6802	814	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	-
GCF_018603435.1	s__Chryseobacterium sp013153155	81.6528	833	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.28	96.28	0.93	0.93	2	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	81.5092	778	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
GCF_000813825.1	s__Chryseobacterium taiwanense	81.4912	765	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109935.1	s__Chryseobacterium taichungense	81.4589	778	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333355.1	s__Chryseobacterium sp000333355	81.2982	620	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927265.1	s__Chryseobacterium cheonjiense	81.0385	789	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142785.1	s__Chryseobacterium carnipullorum	80.5788	676	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.36	98.32	0.90	0.88	5	-
GCF_000737765.1	s__Chryseobacterium vrystaatense	80.225	682	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.86	98.86	0.93	0.93	2	-
GCF_900128945.1	s__Chryseobacterium sp900128945	80.1309	692	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.14	97.03	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:38,170] [INFO] GTDB search result was written to GCF_000430825.1_ASM43082v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:38,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:38,175] [INFO] DFAST_QC result json was written to GCF_000430825.1_ASM43082v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:38,175] [INFO] DFAST_QC completed!
[2024-01-24 13:44:38,175] [INFO] Total running time: 0h1m41s