[2024-01-24 12:31:05,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:05,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:05,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg93949d1e-5ae3-4ea9-8204-0f15623f0214/dqc_reference
[2024-01-24 12:31:06,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:06,489] [INFO] Task started: Prodigal
[2024-01-24 12:31:06,490] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c6e02ee-4c12-43de-ad28-a2dfe2b6dadf/GCF_016598775.1_ASM1659877v1_genomic.fna.gz | prodigal -d GCF_016598775.1_ASM1659877v1_genomic.fna/cds.fna -a GCF_016598775.1_ASM1659877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:14,373] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:14,374] [INFO] Task started: HMMsearch
[2024-01-24 12:31:14,374] [INFO] Running command: hmmsearch --tblout GCF_016598775.1_ASM1659877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93949d1e-5ae3-4ea9-8204-0f15623f0214/dqc_reference/reference_markers.hmm GCF_016598775.1_ASM1659877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:14,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:14,615] [INFO] Found 6/6 markers.
[2024-01-24 12:31:14,639] [INFO] Query marker FASTA was written to GCF_016598775.1_ASM1659877v1_genomic.fna/markers.fasta
[2024-01-24 12:31:14,639] [INFO] Task started: Blastn
[2024-01-24 12:31:14,640] [INFO] Running command: blastn -query GCF_016598775.1_ASM1659877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93949d1e-5ae3-4ea9-8204-0f15623f0214/dqc_reference/reference_markers.fasta -out GCF_016598775.1_ASM1659877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:15,737] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:15,746] [INFO] Selected 20 target genomes.
[2024-01-24 12:31:15,746] [INFO] Target genome list was writen to GCF_016598775.1_ASM1659877v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:15,770] [INFO] Task started: fastANI
[2024-01-24 12:31:15,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c6e02ee-4c12-43de-ad28-a2dfe2b6dadf/GCF_016598775.1_ASM1659877v1_genomic.fna.gz --refList GCF_016598775.1_ASM1659877v1_genomic.fna/target_genomes.txt --output GCF_016598775.1_ASM1659877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:27,893] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:27,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93949d1e-5ae3-4ea9-8204-0f15623f0214/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:27,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93949d1e-5ae3-4ea9-8204-0f15623f0214/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:27,910] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:27,910] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:27,910] [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
Actinomyces weissii	strain=CCUG 61299	GCA_016598775.1	675090	675090	type	True	100.0	854	854	95	conclusive
Actinomyces trachealis	strain=zg-993	GCA_015711475.2	2763540	2763540	type	True	84.337	568	854	95	below_threshold
Actinomyces bovis	strain=NCTC11535	GCA_900444995.1	1658	1658	type	True	82.0131	505	854	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	80.9588	419	854	95	below_threshold
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	80.9443	457	854	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	80.7534	425	854	95	below_threshold
Actinomyces succiniciruminis	strain=AM4	GCA_900002405.2	1522002	1522002	type	True	80.6836	400	854	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	80.6475	455	854	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.5892	337	854	95	below_threshold
Actinomyces oris	strain=CCUG 34288	GCA_006546825.1	544580	544580	suspected-type	True	80.5865	418	854	95	below_threshold
Actinomyces slackii	strain=NCTC11923	GCA_900637295.1	52774	52774	type	True	80.5436	419	854	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	80.5217	370	854	95	below_threshold
Actinomyces faecalis	strain=ZJ34	GCA_013184985.2	2722820	2722820	type	True	80.468	375	854	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	80.1935	377	854	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	80.0874	382	854	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	79.9594	340	854	95	below_threshold
Actinomyces oricola	strain=R5292	GCA_004104015.1	206043	206043	type	True	79.76	360	854	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.1453	125	854	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.9955	172	854	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	76.8661	133	854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:27,913] [INFO] DFAST Taxonomy check result was written to GCF_016598775.1_ASM1659877v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:27,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:27,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:27,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93949d1e-5ae3-4ea9-8204-0f15623f0214/dqc_reference/checkm_data
[2024-01-24 12:31:27,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:27,953] [INFO] Task started: CheckM
[2024-01-24 12:31:27,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016598775.1_ASM1659877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016598775.1_ASM1659877v1_genomic.fna/checkm_input GCF_016598775.1_ASM1659877v1_genomic.fna/checkm_result
[2024-01-24 12:31:54,875] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:54,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:54,897] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:54,897] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:54,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016598775.1_ASM1659877v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:54,898] [INFO] Task started: Blastn
[2024-01-24 12:31:54,898] [INFO] Running command: blastn -query GCF_016598775.1_ASM1659877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93949d1e-5ae3-4ea9-8204-0f15623f0214/dqc_reference/reference_markers_gtdb.fasta -out GCF_016598775.1_ASM1659877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:56,494] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:56,498] [INFO] Selected 20 target genomes.
[2024-01-24 12:31:56,498] [INFO] Target genome list was writen to GCF_016598775.1_ASM1659877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:56,516] [INFO] Task started: fastANI
[2024-01-24 12:31:56,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c6e02ee-4c12-43de-ad28-a2dfe2b6dadf/GCF_016598775.1_ASM1659877v1_genomic.fna.gz --refList GCF_016598775.1_ASM1659877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016598775.1_ASM1659877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:08,223] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:08,251] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:08,252] [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_016598775.1	s__Actinomyces weissii	100.0	854	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015711475.1	s__Actinomyces sp015711475	84.3331	570	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.54	99.54	0.99	0.99	2	-
GCA_900444995.1	s__Actinomyces bovis	81.9506	503	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900103885.1	s__Actinomyces ruminicola	80.9588	419	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_017592395.1	s__Actinomyces bowdenii	80.9247	457	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.11	99.11	0.96	0.96	2	-
GCF_014595995.2	s__Actinomyces sp011751985	80.8676	394	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	-
GCF_013415415.1	s__Actinomyces bowdenii_B	80.8487	410	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	0.98	0.98	2	-
GCF_002999235.1	s__Actinomyces sp002999235	80.826	432	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.35	98.35	0.96	0.96	2	-
GCF_001929375.1	s__Actinomyces oris_B	80.7211	407	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_900002405.1	s__Actinomyces succiniciruminis	80.6828	400	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.30	98.26	0.87	0.86	3	-
GCF_000429225.1	s__Actinomyces dentalis	80.6613	454	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCF_001278845.1	s__Actinomyces sp001278845	80.6572	438	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553935.1	s__Actinomyces oris_A	80.6186	419	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.65	97.48	0.94	0.93	4	-
GCF_006546825.1	s__Actinomyces oris	80.5873	418	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
GCF_001937445.1	s__Actinomyces oris_C	80.5609	408	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.06	96.78	0.88	0.86	9	-
GCF_900637295.1	s__Actinomyces slackii	80.5298	420	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013184985.2	s__Actinomyces sp013185035	80.4555	375	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_000159035.1	s__Actinomyces urogenitalis	80.2088	376	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.08	98.90	0.93	0.88	7	-
GCF_001553565.1	s__Actinomyces radicidentis	80.1017	381	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355765.1	s__Actinomyces haliotis	79.9595	340	854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:08,254] [INFO] GTDB search result was written to GCF_016598775.1_ASM1659877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:08,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:08,260] [INFO] DFAST_QC result json was written to GCF_016598775.1_ASM1659877v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:08,261] [INFO] DFAST_QC completed!
[2024-01-24 12:32:08,261] [INFO] Total running time: 0h1m3s