[2024-01-24 13:40:55,585] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fc03d2c-5584-4867-b171-3b9fc2985206/dqc_reference
[2024-01-24 13:40:56,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,875] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg09691888-349b-4af9-925e-780a5ef8218b/GCF_000430845.1_ASM43084v1_genomic.fna.gz | prodigal -d GCF_000430845.1_ASM43084v1_genomic.fna/cds.fna -a GCF_000430845.1_ASM43084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:11,180] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:11,181] [INFO] Task started: HMMsearch
[2024-01-24 13:41:11,181] [INFO] Running command: hmmsearch --tblout GCF_000430845.1_ASM43084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fc03d2c-5584-4867-b171-3b9fc2985206/dqc_reference/reference_markers.hmm GCF_000430845.1_ASM43084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:11,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:11,518] [INFO] Found 6/6 markers.
[2024-01-24 13:41:11,552] [INFO] Query marker FASTA was written to GCF_000430845.1_ASM43084v1_genomic.fna/markers.fasta
[2024-01-24 13:41:11,552] [INFO] Task started: Blastn
[2024-01-24 13:41:11,552] [INFO] Running command: blastn -query GCF_000430845.1_ASM43084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc03d2c-5584-4867-b171-3b9fc2985206/dqc_reference/reference_markers.fasta -out GCF_000430845.1_ASM43084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:12,135] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:12,138] [INFO] Selected 23 target genomes.
[2024-01-24 13:41:12,138] [INFO] Target genome list was writen to GCF_000430845.1_ASM43084v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:12,147] [INFO] Task started: fastANI
[2024-01-24 13:41:12,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg09691888-349b-4af9-925e-780a5ef8218b/GCF_000430845.1_ASM43084v1_genomic.fna.gz --refList GCF_000430845.1_ASM43084v1_genomic.fna/target_genomes.txt --output GCF_000430845.1_ASM43084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:33,387] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:33,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fc03d2c-5584-4867-b171-3b9fc2985206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:33,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fc03d2c-5584-4867-b171-3b9fc2985206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:33,400] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:33,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:33,400] [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 gregarium	strain=DSM 19109	GCA_000430845.1	456299	456299	type	True	100.0	1453	1456	95	conclusive
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	80.5706	745	1456	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.4988	761	1456	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	80.3236	719	1456	95	below_threshold
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	80.2336	699	1456	95	below_threshold
Chryseobacterium hispalense	strain=DSM 25574	GCA_000708615.2	1453492	1453492	type	True	80.157	727	1456	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	80.1545	735	1456	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	80.0095	670	1456	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	79.9601	708	1456	95	below_threshold
Chryseobacterium taichungense	strain=DSM 17453	GCA_900109935.1	295069	295069	type	True	79.9453	713	1456	95	below_threshold
Chryseobacterium takakiae	strain=DSM 26898	GCA_900129385.1	1302685	1302685	type	True	79.9424	708	1456	95	below_threshold
Chryseobacterium hagamense	strain=NBRC 105253	GCA_007991455.1	395935	395935	type	True	79.7048	710	1456	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.6664	629	1456	95	below_threshold
Chryseobacterium carnipullorum	strain=DSM 25581	GCA_900142785.1	1124835	1124835	type	True	79.4733	594	1456	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	79.4401	592	1456	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	79.4314	576	1456	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	79.3628	596	1456	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	79.2729	594	1456	95	below_threshold
Chryseobacterium vrystaatense	strain=LMG 22846	GCA_000737765.1	307480	307480	type	True	79.1929	581	1456	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	77.2703	107	1456	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.2143	153	1456	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.2056	152	1456	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,402] [INFO] DFAST Taxonomy check result was written to GCF_000430845.1_ASM43084v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:33,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:33,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:33,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fc03d2c-5584-4867-b171-3b9fc2985206/dqc_reference/checkm_data
[2024-01-24 13:41:33,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:33,446] [INFO] Task started: CheckM
[2024-01-24 13:41:33,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430845.1_ASM43084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430845.1_ASM43084v1_genomic.fna/checkm_input GCF_000430845.1_ASM43084v1_genomic.fna/checkm_result
[2024-01-24 13:42:15,690] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:15,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,706] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:15,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:15,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430845.1_ASM43084v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:15,707] [INFO] Task started: Blastn
[2024-01-24 13:42:15,707] [INFO] Running command: blastn -query GCF_000430845.1_ASM43084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc03d2c-5584-4867-b171-3b9fc2985206/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430845.1_ASM43084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:16,545] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:16,548] [INFO] Selected 17 target genomes.
[2024-01-24 13:42:16,548] [INFO] Target genome list was writen to GCF_000430845.1_ASM43084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:16,566] [INFO] Task started: fastANI
[2024-01-24 13:42:16,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg09691888-349b-4af9-925e-780a5ef8218b/GCF_000430845.1_ASM43084v1_genomic.fna.gz --refList GCF_000430845.1_ASM43084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430845.1_ASM43084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:32,482] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:32,493] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:32,493] [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_000430845.1	s__Chryseobacterium gregarium	100.0	1453	1456	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_001421435.1	s__Chryseobacterium sp001421435	86.7602	1043	1456	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	80.8895	763	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111495.1	s__Chryseobacterium wanjuense	80.5872	743	1456	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	80.4854	704	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.07	98.07	0.94	0.94	2	-
GCF_000430825.1	s__Chryseobacterium daeguense	80.3441	716	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708615.2	s__Chryseobacterium hispalense	80.1626	725	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.96	98.96	0.90	0.90	2	-
GCF_900156825.1	s__Chryseobacterium gambrini	80.1347	738	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_018603435.1	s__Chryseobacterium sp013153155	80.12	711	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.28	96.28	0.93	0.93	2	-
GCA_002434285.1	s__Chryseobacterium sp002434285	80.1065	639	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099685.1	s__Chryseobacterium taeanense	79.9977	671	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329705.1	s__Chryseobacterium sp008329705	79.9887	749	1456	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	79.9725	705	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	-
GCF_000333355.1	s__Chryseobacterium sp000333355	79.8679	597	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991455.1	s__Chryseobacterium hagamense	79.734	708	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927325.1	s__Chryseobacterium antibioticum	79.2685	595	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737765.1	s__Chryseobacterium vrystaatense	79.2012	581	1456	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.86	98.86	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:32,494] [INFO] GTDB search result was written to GCF_000430845.1_ASM43084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:32,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:32,498] [INFO] DFAST_QC result json was written to GCF_000430845.1_ASM43084v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:32,498] [INFO] DFAST_QC completed!
[2024-01-24 13:42:32,498] [INFO] Total running time: 0h1m37s