[2024-01-24 12:47:28,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:28,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:28,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg28cab644-4318-43ac-a323-dc0aaca1a433/dqc_reference
[2024-01-24 12:47:29,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:29,444] [INFO] Task started: Prodigal
[2024-01-24 12:47:29,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg25c5ad07-56f2-407b-a928-1964a7dcdba8/GCF_000023925.1_ASM2392v1_genomic.fna.gz | prodigal -d GCF_000023925.1_ASM2392v1_genomic.fna/cds.fna -a GCF_000023925.1_ASM2392v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:38,804] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:38,804] [INFO] Task started: HMMsearch
[2024-01-24 12:47:38,804] [INFO] Running command: hmmsearch --tblout GCF_000023925.1_ASM2392v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28cab644-4318-43ac-a323-dc0aaca1a433/dqc_reference/reference_markers.hmm GCF_000023925.1_ASM2392v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:39,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:39,040] [INFO] Found 6/6 markers.
[2024-01-24 12:47:39,064] [INFO] Query marker FASTA was written to GCF_000023925.1_ASM2392v1_genomic.fna/markers.fasta
[2024-01-24 12:47:39,065] [INFO] Task started: Blastn
[2024-01-24 12:47:39,065] [INFO] Running command: blastn -query GCF_000023925.1_ASM2392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28cab644-4318-43ac-a323-dc0aaca1a433/dqc_reference/reference_markers.fasta -out GCF_000023925.1_ASM2392v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:40,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:40,238] [INFO] Selected 15 target genomes.
[2024-01-24 12:47:40,239] [INFO] Target genome list was writen to GCF_000023925.1_ASM2392v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:40,243] [INFO] Task started: fastANI
[2024-01-24 12:47:40,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg25c5ad07-56f2-407b-a928-1964a7dcdba8/GCF_000023925.1_ASM2392v1_genomic.fna.gz --refList GCF_000023925.1_ASM2392v1_genomic.fna/target_genomes.txt --output GCF_000023925.1_ASM2392v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:49,968] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:49,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28cab644-4318-43ac-a323-dc0aaca1a433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:49,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28cab644-4318-43ac-a323-dc0aaca1a433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:49,996] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:47:49,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:49,997] [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
Kytococcus sedentarius	strain=DSM 20547	GCA_000023925.1	1276	1276	type	True	100.0	927	928	95	conclusive
Kytococcus sedentarius	strain=FDAARGOS_1061	GCA_016127495.1	1276	1276	type	True	99.9966	925	928	95	conclusive
Kytococcus sedentarius	strain=NCTC11040	GCA_900452405.1	1276	1276	type	True	99.9945	926	928	95	conclusive
Kytococcus aerolatus	strain=DSM 22179	GCA_900187395.1	592308	592308	type	True	84.0589	626	928	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	78.9178	316	928	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	78.4596	282	928	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	78.3578	290	928	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	78.2164	290	928	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.1907	290	928	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	78.1312	294	928	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	78.0738	264	928	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	78.0539	295	928	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	77.9114	271	928	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.8912	189	928	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	77.8389	242	928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:49,998] [INFO] DFAST Taxonomy check result was written to GCF_000023925.1_ASM2392v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:49,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:49,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:49,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28cab644-4318-43ac-a323-dc0aaca1a433/dqc_reference/checkm_data
[2024-01-24 12:47:50,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:50,029] [INFO] Task started: CheckM
[2024-01-24 12:47:50,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000023925.1_ASM2392v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000023925.1_ASM2392v1_genomic.fna/checkm_input GCF_000023925.1_ASM2392v1_genomic.fna/checkm_result
[2024-01-24 12:48:44,756] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:44,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:44,826] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:44,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:44,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000023925.1_ASM2392v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:44,827] [INFO] Task started: Blastn
[2024-01-24 12:48:44,828] [INFO] Running command: blastn -query GCF_000023925.1_ASM2392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28cab644-4318-43ac-a323-dc0aaca1a433/dqc_reference/reference_markers_gtdb.fasta -out GCF_000023925.1_ASM2392v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:46,699] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:46,703] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:46,704] [INFO] Target genome list was writen to GCF_000023925.1_ASM2392v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:46,713] [INFO] Task started: fastANI
[2024-01-24 12:48:46,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg25c5ad07-56f2-407b-a928-1964a7dcdba8/GCF_000023925.1_ASM2392v1_genomic.fna.gz --refList GCF_000023925.1_ASM2392v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000023925.1_ASM2392v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:56,044] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:56,059] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:56,060] [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_000023925.1	s__Kytococcus sedentarius	100.0	927	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kytococcus	95.0	98.33	96.37	0.94	0.84	5	conclusive
GCF_002847825.1	s__Kytococcus schroeteri	84.4726	605	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kytococcus	95.0	99.14	99.06	0.95	0.94	3	-
GCF_900187395.1	s__Kytococcus aerolatus	84.0584	625	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kytococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	78.8786	321	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	78.6095	303	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.4847	303	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337125.1	s__Serinicoccus chungangensis	78.2549	287	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721155.3	s__Marihabitans melonis	78.044	280	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_004153545.1	s__Serinicoccus sediminis	78.0342	296	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483745.1	s__Serinicoccus chungangensis_A	78.0236	292	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570945.1	s__Janibacter anophelis	77.973	249	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_011326735.1	s__Phycicoccus endophyticus	77.8517	240	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	-
GCA_012515595.1	s__Ornithinicoccus sp012515595	77.6931	244	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	77.5762	281	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763705.1	s__Phycicoccus sp014763705	77.5536	207	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:56,062] [INFO] GTDB search result was written to GCF_000023925.1_ASM2392v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:56,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:56,066] [INFO] DFAST_QC result json was written to GCF_000023925.1_ASM2392v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:56,066] [INFO] DFAST_QC completed!
[2024-01-24 12:48:56,066] [INFO] Total running time: 0h1m28s