[2024-01-24 13:31:33,491] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg95a29671-21a8-4d6a-b45c-2a24c681bf54/dqc_reference
[2024-01-24 13:31:34,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,826] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,827] [INFO] Running command: gunzip -c /var/lib/cwl/stgd674cdb6-16c3-4c9d-b134-6b38ea024f4d/GCF_015240065.1_ASM1524006v1_genomic.fna.gz | prodigal -d GCF_015240065.1_ASM1524006v1_genomic.fna/cds.fna -a GCF_015240065.1_ASM1524006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:40,960] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:40,960] [INFO] Task started: HMMsearch
[2024-01-24 13:31:40,961] [INFO] Running command: hmmsearch --tblout GCF_015240065.1_ASM1524006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95a29671-21a8-4d6a-b45c-2a24c681bf54/dqc_reference/reference_markers.hmm GCF_015240065.1_ASM1524006v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:41,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:41,194] [INFO] Found 6/6 markers.
[2024-01-24 13:31:41,219] [INFO] Query marker FASTA was written to GCF_015240065.1_ASM1524006v1_genomic.fna/markers.fasta
[2024-01-24 13:31:41,219] [INFO] Task started: Blastn
[2024-01-24 13:31:41,219] [INFO] Running command: blastn -query GCF_015240065.1_ASM1524006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95a29671-21a8-4d6a-b45c-2a24c681bf54/dqc_reference/reference_markers.fasta -out GCF_015240065.1_ASM1524006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:42,204] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:42,210] [INFO] Selected 28 target genomes.
[2024-01-24 13:31:42,210] [INFO] Target genome list was writen to GCF_015240065.1_ASM1524006v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:42,231] [INFO] Task started: fastANI
[2024-01-24 13:31:42,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgd674cdb6-16c3-4c9d-b134-6b38ea024f4d/GCF_015240065.1_ASM1524006v1_genomic.fna.gz --refList GCF_015240065.1_ASM1524006v1_genomic.fna/target_genomes.txt --output GCF_015240065.1_ASM1524006v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:58,081] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:58,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95a29671-21a8-4d6a-b45c-2a24c681bf54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:58,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95a29671-21a8-4d6a-b45c-2a24c681bf54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:58,107] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:58,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:58,107] [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
Nanchangia anserum	strain=C64	GCA_015240065.1	2692125	2692125	type	True	100.0	635	635	95	conclusive
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	77.9683	124	635	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	77.5493	150	635	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	77.4036	132	635	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	77.4029	116	635	95	below_threshold
Actinomyces howellii	strain=NCTC11636	GCA_900637165.1	52771	52771	type	True	77.4028	132	635	95	below_threshold
Actinomyces slackii	strain=NCTC11923	GCA_900637295.1	52774	52774	type	True	77.3304	107	635	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	77.1968	120	635	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	77.0534	130	635	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	77.0144	128	635	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	77.0032	130	635	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	76.9871	114	635	95	below_threshold
Brevibacterium casei	strain=FDAARGOS_936	GCA_016026595.1	33889	33889	type	True	76.925	103	635	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	76.8698	125	635	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	76.8431	95	635	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.8116	116	635	95	below_threshold
Actinomyces slackii	strain=ATCC 49928	GCA_000428685.1	52774	52774	type	True	76.7986	98	635	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	76.7813	89	635	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	76.6961	119	635	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	76.6737	90	635	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	76.6088	110	635	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	76.5801	113	635	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	76.5443	122	635	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	76.5188	110	635	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.3226	100	635	95	below_threshold
Brachybacterium nesterenkovii	strain=CIP104813	GCA_900163655.1	47847	47847	type	True	76.2923	97	635	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	76.2416	100	635	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	76.0248	88	635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:58,109] [INFO] DFAST Taxonomy check result was written to GCF_015240065.1_ASM1524006v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:58,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:58,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:58,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95a29671-21a8-4d6a-b45c-2a24c681bf54/dqc_reference/checkm_data
[2024-01-24 13:31:58,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:58,133] [INFO] Task started: CheckM
[2024-01-24 13:31:58,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015240065.1_ASM1524006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015240065.1_ASM1524006v1_genomic.fna/checkm_input GCF_015240065.1_ASM1524006v1_genomic.fna/checkm_result
[2024-01-24 13:32:21,567] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:21,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:21,582] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:21,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:21,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015240065.1_ASM1524006v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:21,583] [INFO] Task started: Blastn
[2024-01-24 13:32:21,584] [INFO] Running command: blastn -query GCF_015240065.1_ASM1524006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95a29671-21a8-4d6a-b45c-2a24c681bf54/dqc_reference/reference_markers_gtdb.fasta -out GCF_015240065.1_ASM1524006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:23,017] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:23,020] [INFO] Selected 25 target genomes.
[2024-01-24 13:32:23,021] [INFO] Target genome list was writen to GCF_015240065.1_ASM1524006v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:23,041] [INFO] Task started: fastANI
[2024-01-24 13:32:23,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgd674cdb6-16c3-4c9d-b134-6b38ea024f4d/GCF_015240065.1_ASM1524006v1_genomic.fna.gz --refList GCF_015240065.1_ASM1524006v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015240065.1_ASM1524006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:36,349] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:36,374] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:36,375] [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_015240065.1	s__UMGS822 sp015240065	100.0	635	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__UMGS822	95.0	99.96	99.96	1.00	1.00	2	conclusive
GCA_900545825.1	s__UMGS822 sp900545825	79.859	321	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__UMGS822	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208035.1	s__Pauljensenia hyovaginalis	78.0566	125	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.48	95.48	0.88	0.88	2	-
GCF_000411415.1	s__Pauljensenia sp000411415	77.7744	103	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.95	97.15	0.96	0.94	6	-
GCF_001553935.1	s__Actinomyces oris_A	77.4735	113	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.65	97.48	0.94	0.93	4	-
GCA_001072465.1	s__Pauljensenia sp001072465	77.451	114	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_900637975.1	s__Actinomyces viscosus	77.2819	132	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900637295.1	s__Actinomyces slackii	77.2513	106	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001929375.1	s__Actinomyces oris_B	77.2228	112	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_011752065.1	s__Actinomyces sp011752065	77.1413	123	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001838165.1	s__Pauljensenia sp001838165	77.124	114	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCF_000295095.1	s__Actinomyces timonensis	77.1012	123	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155435.1	s__Pauljensenia provencensis	76.8698	125	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	96.43	0.91	0.91	2	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	76.7661	144	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014360395.1	s__Actinotalea sp014360395	76.7624	86	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837175.1	s__Cellulomonas sp014837175	76.7412	111	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	76.7287	133	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	76.6312	136	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	76.6088	110	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001750215.1	s__Xylanimonas variabilis_A	76.5027	116	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	76.4264	129	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012952065.1	s__Cellulomonas fimi_A	76.3728	102	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989805.1	s__Cellulomonas xylanilytica	76.2088	105	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592125.1	s__Microbacterium hominis	75.9816	86	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.42	0.92	0.89	6	-
GCA_012514835.1	s__JAAYZM01 sp012514835	75.6148	57	635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__JAAYZM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:36,377] [INFO] GTDB search result was written to GCF_015240065.1_ASM1524006v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:36,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:36,384] [INFO] DFAST_QC result json was written to GCF_015240065.1_ASM1524006v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:36,384] [INFO] DFAST_QC completed!
[2024-01-24 13:32:36,385] [INFO] Total running time: 0h1m3s