[2024-01-24 10:57:13,087] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,094] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1e8146a-b042-4388-839b-4414dc0c88ab/dqc_reference
[2024-01-24 10:57:14,516] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,517] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,517] [INFO] Running command: gunzip -c /var/lib/cwl/stgd578c6c7-a7c4-4c5e-aa74-2245986a1d0f/GCF_024055725.1_ASM2405572v1_genomic.fna.gz | prodigal -d GCF_024055725.1_ASM2405572v1_genomic.fna/cds.fna -a GCF_024055725.1_ASM2405572v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:36,863] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:36,863] [INFO] Task started: HMMsearch
[2024-01-24 10:57:36,863] [INFO] Running command: hmmsearch --tblout GCF_024055725.1_ASM2405572v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1e8146a-b042-4388-839b-4414dc0c88ab/dqc_reference/reference_markers.hmm GCF_024055725.1_ASM2405572v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:37,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:37,363] [INFO] Found 6/6 markers.
[2024-01-24 10:57:37,431] [INFO] Query marker FASTA was written to GCF_024055725.1_ASM2405572v1_genomic.fna/markers.fasta
[2024-01-24 10:57:37,431] [INFO] Task started: Blastn
[2024-01-24 10:57:37,431] [INFO] Running command: blastn -query GCF_024055725.1_ASM2405572v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1e8146a-b042-4388-839b-4414dc0c88ab/dqc_reference/reference_markers.fasta -out GCF_024055725.1_ASM2405572v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:38,906] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:38,909] [INFO] Selected 22 target genomes.
[2024-01-24 10:57:38,910] [INFO] Target genome list was writen to GCF_024055725.1_ASM2405572v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:38,923] [INFO] Task started: fastANI
[2024-01-24 10:57:38,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgd578c6c7-a7c4-4c5e-aa74-2245986a1d0f/GCF_024055725.1_ASM2405572v1_genomic.fna.gz --refList GCF_024055725.1_ASM2405572v1_genomic.fna/target_genomes.txt --output GCF_024055725.1_ASM2405572v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:17,134] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:17,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1e8146a-b042-4388-839b-4414dc0c88ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:17,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1e8146a-b042-4388-839b-4414dc0c88ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:17,153] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:17,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:17,154] [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 spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	100.0	2638	2643	95	conclusive
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	86.7376	1790	2643	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	81.1183	1396	2643	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	78.9626	1176	2643	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	78.8783	819	2643	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	78.8403	1014	2643	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	78.81	1240	2643	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	78.7549	1045	2643	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	78.7079	1140	2643	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	78.6968	1134	2643	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	78.6562	1088	2643	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	78.6039	1089	2643	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	78.5119	1022	2643	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	78.4835	932	2643	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	78.4397	950	2643	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	78.4077	1102	2643	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	78.3384	1102	2643	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	78.2376	901	2643	95	below_threshold
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	76.7021	518	2643	95	below_threshold
Actinospica robiniae	strain=DSM 44927	GCA_000504285.1	304901	304901	type	True	76.4264	693	2643	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	76.2227	349	2643	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.1022	382	2643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:17,156] [INFO] DFAST Taxonomy check result was written to GCF_024055725.1_ASM2405572v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:17,156] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:17,156] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:17,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1e8146a-b042-4388-839b-4414dc0c88ab/dqc_reference/checkm_data
[2024-01-24 10:58:17,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:17,231] [INFO] Task started: CheckM
[2024-01-24 10:58:17,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024055725.1_ASM2405572v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024055725.1_ASM2405572v1_genomic.fna/checkm_input GCF_024055725.1_ASM2405572v1_genomic.fna/checkm_result
[2024-01-24 10:59:26,890] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:26,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:26,913] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:26,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:26,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024055725.1_ASM2405572v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:26,914] [INFO] Task started: Blastn
[2024-01-24 10:59:26,914] [INFO] Running command: blastn -query GCF_024055725.1_ASM2405572v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1e8146a-b042-4388-839b-4414dc0c88ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_024055725.1_ASM2405572v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:29,197] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:29,202] [INFO] Selected 30 target genomes.
[2024-01-24 10:59:29,202] [INFO] Target genome list was writen to GCF_024055725.1_ASM2405572v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:29,241] [INFO] Task started: fastANI
[2024-01-24 10:59:29,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgd578c6c7-a7c4-4c5e-aa74-2245986a1d0f/GCF_024055725.1_ASM2405572v1_genomic.fna.gz --refList GCF_024055725.1_ASM2405572v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024055725.1_ASM2405572v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:16,058] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:16,085] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:00:16,085] [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	81.079	1405	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinoallomurus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589885.1	s__Thermomonospora amylolytica	79.2542	929	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCA_003001795.1	s__Actinomadura_B viridilutea	79.0501	971	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004349245.1	s__Spirillospora sp004349245	78.9886	937	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923365.1	s__Spirillospora montaniterrae	78.9886	1166	2643	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	78.9285	877	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	78.8613	1140	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552195.1	s__Spirillospora latina	78.8061	1030	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900188105.1	s__Spirillospora mexicana	78.7931	1053	2643	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	78.788	914	2643	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_014323705.1	s__Actinomadura_C alba	78.7244	908	2643	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_013409365.1	s__Spirillospora luteofluorescens	78.7204	1115	2643	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	78.7169	1162	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_001552175.1	s__Spirillospora kijaniata	78.6946	1134	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_000718255.1	s__Spirillospora albida	78.6833	894	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751755.1	s__Spirillospora viridis	78.6612	1085	2643	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	78.6154	942	2643	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	78.6133	1190	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348535.1	s__Spirillospora sp004348535	78.5802	913	2643	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	78.5766	1071	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	-
GCF_014648495.1	s__Spirillospora cremea	78.5148	1069	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374305.1	s__Spirillospora flavalba	78.4893	930	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381885.1	s__Spirillospora atramentaria	78.408	959	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432485.1	s__Spirillospora sp003432485	78.2508	898	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017354375.1	s__Trebonia sp017354375	76.8718	448	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Trebonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	76.7475	613	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117935.1	s__Streptomyces roseicoloratus	76.6878	704	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504285.1	s__Actinospica robiniae	76.4276	689	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024925.1	s__Sanguibacter keddieii	76.2097	350	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383475.1	s__Microbacterium sp000383475	75.8862	229	2643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.27	98.25	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:16,087] [INFO] GTDB search result was written to GCF_024055725.1_ASM2405572v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:16,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:16,092] [INFO] DFAST_QC result json was written to GCF_024055725.1_ASM2405572v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:16,092] [INFO] DFAST_QC completed!
[2024-01-24 11:00:16,092] [INFO] Total running time: 0h3m3s