[2024-01-24 11:27:04,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,677] [INFO] DQC Reference Directory: /var/lib/cwl/stga658d7a3-5db9-4d50-a89b-5b9d6e2a3239/dqc_reference
[2024-01-24 11:27:05,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,907] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg38398e13-7c74-4acc-8176-f4b36e87eb93/GCF_024055795.1_ASM2405579v1_genomic.fna.gz | prodigal -d GCF_024055795.1_ASM2405579v1_genomic.fna/cds.fna -a GCF_024055795.1_ASM2405579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:33,782] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:33,783] [INFO] Task started: HMMsearch
[2024-01-24 11:27:33,783] [INFO] Running command: hmmsearch --tblout GCF_024055795.1_ASM2405579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga658d7a3-5db9-4d50-a89b-5b9d6e2a3239/dqc_reference/reference_markers.hmm GCF_024055795.1_ASM2405579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:34,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:34,154] [INFO] Found 6/6 markers.
[2024-01-24 11:27:34,223] [INFO] Query marker FASTA was written to GCF_024055795.1_ASM2405579v1_genomic.fna/markers.fasta
[2024-01-24 11:27:34,223] [INFO] Task started: Blastn
[2024-01-24 11:27:34,223] [INFO] Running command: blastn -query GCF_024055795.1_ASM2405579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga658d7a3-5db9-4d50-a89b-5b9d6e2a3239/dqc_reference/reference_markers.fasta -out GCF_024055795.1_ASM2405579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:35,498] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:35,501] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:35,502] [INFO] Target genome list was writen to GCF_024055795.1_ASM2405579v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:35,515] [INFO] Task started: fastANI
[2024-01-24 11:27:35,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg38398e13-7c74-4acc-8176-f4b36e87eb93/GCF_024055795.1_ASM2405579v1_genomic.fna.gz --refList GCF_024055795.1_ASM2405579v1_genomic.fna/target_genomes.txt --output GCF_024055795.1_ASM2405579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:28:08,978] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:08,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga658d7a3-5db9-4d50-a89b-5b9d6e2a3239/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:28:08,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga658d7a3-5db9-4d50-a89b-5b9d6e2a3239/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:28:08,997] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:28:08,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:28:08,998] [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
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	100.0	3049	3053	95	conclusive
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	86.7501	1790	3053	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	81.0987	1469	3053	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	78.7003	1149	3053	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	78.572	1102	3053	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	78.4521	990	3053	95	below_threshold
Actinomadura logoneensis	strain=NEAU-G17	GCA_003428695.1	2293572	2293572	type	True	78.4376	908	3053	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	78.4319	1103	3053	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	78.4294	1254	3053	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	78.4128	1118	3053	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	78.3208	1042	3053	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	78.3089	1186	3053	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	78.2875	1101	3053	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	78.2797	1008	3053	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	78.2125	1051	3053	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	78.2039	976	3053	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	78.129	933	3053	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	76.877	475	3053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:28:09,000] [INFO] DFAST Taxonomy check result was written to GCF_024055795.1_ASM2405579v1_genomic.fna/tc_result.tsv
[2024-01-24 11:28:09,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:28:09,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:28:09,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga658d7a3-5db9-4d50-a89b-5b9d6e2a3239/dqc_reference/checkm_data
[2024-01-24 11:28:09,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:28:09,087] [INFO] Task started: CheckM
[2024-01-24 11:28:09,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024055795.1_ASM2405579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024055795.1_ASM2405579v1_genomic.fna/checkm_input GCF_024055795.1_ASM2405579v1_genomic.fna/checkm_result
[2024-01-24 11:29:34,551] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:34,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:34,577] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:34,577] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:34,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024055795.1_ASM2405579v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:34,578] [INFO] Task started: Blastn
[2024-01-24 11:29:34,578] [INFO] Running command: blastn -query GCF_024055795.1_ASM2405579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga658d7a3-5db9-4d50-a89b-5b9d6e2a3239/dqc_reference/reference_markers_gtdb.fasta -out GCF_024055795.1_ASM2405579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:36,656] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:36,660] [INFO] Selected 22 target genomes.
[2024-01-24 11:29:36,660] [INFO] Target genome list was writen to GCF_024055795.1_ASM2405579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:36,692] [INFO] Task started: fastANI
[2024-01-24 11:29:36,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg38398e13-7c74-4acc-8176-f4b36e87eb93/GCF_024055795.1_ASM2405579v1_genomic.fna.gz --refList GCF_024055795.1_ASM2405579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024055795.1_ASM2405579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:30:14,032] [INFO] Task succeeded: fastANI
[2024-01-24 11:30:14,052] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:30:14,052] [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_006716425.1	s__Actinoallomurus bryophytorum	81.1035	1468	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinoallomurus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323665.1	s__Actinomadura_C sp014323665	78.8707	854	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323705.1	s__Actinomadura_C alba	78.736	942	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923365.1	s__Spirillospora montaniterrae	78.6588	1163	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	78.5915	1159	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289645.1	s__Actinomadura_D craniellae	78.5658	950	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013211575.1	s__Spirillospora verrucosospora	78.533	1251	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_900659615.1	s__Spirillospora fibrosa	78.5117	1131	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	78.5053	1148	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348665.1	s__Spirillospora sp004348665	78.4947	859	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348335.1	s__Spirillospora bangladeshensis	78.4727	988	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	78.4266	1107	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349245.1	s__Spirillospora sp004349245	78.4128	933	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716765.1	s__Spirillospora hallensis	78.4024	929	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009793335.1	s__Spirillospora sp009793335	78.4005	1191	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552175.1	s__Spirillospora kijaniata	78.3951	1123	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_014648675.1	s__Spirillospora livida	78.2876	1018	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
GCF_006547145.1	s__Spirillospora sp006547145	78.2721	1102	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	78.2592	1151	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_004349215.1	s__Spirillospora rubrisoli	78.2315	1020	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425065.1	s__Spirillospora rifamycini	78.1961	1058	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	-
GCF_000381885.1	s__Spirillospora atramentaria	78.1263	934	3053	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:30:14,054] [INFO] GTDB search result was written to GCF_024055795.1_ASM2405579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:30:14,054] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:30:14,058] [INFO] DFAST_QC result json was written to GCF_024055795.1_ASM2405579v1_genomic.fna/dqc_result.json
[2024-01-24 11:30:14,059] [INFO] DFAST_QC completed!
[2024-01-24 11:30:14,059] [INFO] Total running time: 0h3m9s