[2024-01-24 10:47:06,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg57212554-58e0-45e6-9956-6dfa93c02514/dqc_reference
[2024-01-24 10:47:12,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,812] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,813] [INFO] Running command: gunzip -c /var/lib/cwl/stgd43bef24-f620-47ad-9147-ecfaeed9f891/GCF_006716765.1_ASM671676v1_genomic.fna.gz | prodigal -d GCF_006716765.1_ASM671676v1_genomic.fna/cds.fna -a GCF_006716765.1_ASM671676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:30,477] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:30,477] [INFO] Task started: HMMsearch
[2024-01-24 10:47:30,477] [INFO] Running command: hmmsearch --tblout GCF_006716765.1_ASM671676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57212554-58e0-45e6-9956-6dfa93c02514/dqc_reference/reference_markers.hmm GCF_006716765.1_ASM671676v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:30,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:30,861] [INFO] Found 6/6 markers.
[2024-01-24 10:47:30,912] [INFO] Query marker FASTA was written to GCF_006716765.1_ASM671676v1_genomic.fna/markers.fasta
[2024-01-24 10:47:30,912] [INFO] Task started: Blastn
[2024-01-24 10:47:30,912] [INFO] Running command: blastn -query GCF_006716765.1_ASM671676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57212554-58e0-45e6-9956-6dfa93c02514/dqc_reference/reference_markers.fasta -out GCF_006716765.1_ASM671676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:32,195] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:32,199] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:32,200] [INFO] Target genome list was writen to GCF_006716765.1_ASM671676v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:33,314] [INFO] Task started: fastANI
[2024-01-24 10:47:33,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgd43bef24-f620-47ad-9147-ecfaeed9f891/GCF_006716765.1_ASM671676v1_genomic.fna.gz --refList GCF_006716765.1_ASM671676v1_genomic.fna/target_genomes.txt --output GCF_006716765.1_ASM671676v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:18,640] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:18,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57212554-58e0-45e6-9956-6dfa93c02514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:18,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57212554-58e0-45e6-9956-6dfa93c02514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:18,662] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:18,662] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:18,663] [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
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	100.0	2232	2233	95	conclusive
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	85.9383	1527	2233	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	85.8755	1630	2233	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	85.8003	1685	2233	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	85.797	1652	2233	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	85.7368	1703	2233	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	85.6728	1379	2233	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	85.5569	1460	2233	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	85.3681	1400	2233	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	85.3393	1640	2233	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	85.2461	1594	2233	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	84.641	1577	2233	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.4046	1400	2233	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	84.1948	1503	2233	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	84.1879	1558	2233	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.0433	1620	2233	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.5684	1442	2233	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.5246	1319	2233	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.1264	1277	2233	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	80.0249	1015	2233	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	77.2224	770	2233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:18,664] [INFO] DFAST Taxonomy check result was written to GCF_006716765.1_ASM671676v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:18,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:18,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:18,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57212554-58e0-45e6-9956-6dfa93c02514/dqc_reference/checkm_data
[2024-01-24 10:48:18,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:18,726] [INFO] Task started: CheckM
[2024-01-24 10:48:18,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716765.1_ASM671676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716765.1_ASM671676v1_genomic.fna/checkm_input GCF_006716765.1_ASM671676v1_genomic.fna/checkm_result
[2024-01-24 10:49:44,284] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:44,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:44,308] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:44,309] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:44,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716765.1_ASM671676v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:44,310] [INFO] Task started: Blastn
[2024-01-24 10:49:44,310] [INFO] Running command: blastn -query GCF_006716765.1_ASM671676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57212554-58e0-45e6-9956-6dfa93c02514/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716765.1_ASM671676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:46,335] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:46,339] [INFO] Selected 15 target genomes.
[2024-01-24 10:49:46,340] [INFO] Target genome list was writen to GCF_006716765.1_ASM671676v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:46,359] [INFO] Task started: fastANI
[2024-01-24 10:49:46,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgd43bef24-f620-47ad-9147-ecfaeed9f891/GCF_006716765.1_ASM671676v1_genomic.fna.gz --refList GCF_006716765.1_ASM671676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716765.1_ASM671676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:17,627] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:17,644] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:17,644] [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_006716765.1	s__Spirillospora hallensis	100.0	2233	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014648675.1	s__Spirillospora livida	89.1526	1839	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
GCF_004349245.1	s__Spirillospora sp004349245	88.9498	1735	2233	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	88.6792	1549	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348515.1	s__Spirillospora sp004348515	87.4033	1562	2233	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	85.8116	1651	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001552155.1	s__Spirillospora formosensis	85.6455	1382	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005889745.1	s__Spirillospora geliboluensis	85.5016	1468	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409365.1	s__Spirillospora luteofluorescens	85.2504	1648	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008085905.1	s__Spirillospora syzygii	84.5865	1586	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.88	95.88	0.90	0.90	2	-
GCF_008923365.1	s__Spirillospora montaniterrae	84.1835	1505	2233	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	84.1353	1566	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024385.1	s__Thermomonospora curvata	80.0383	1017	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	99.63	99.63	0.99	0.99	2	-
GCF_018476525.1	s__Acrocarpospora sp018476525	77.2292	762	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687885.1	s__Acrocarpospora pleiomorpha	77.1907	748	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:17,645] [INFO] GTDB search result was written to GCF_006716765.1_ASM671676v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:17,646] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:17,650] [INFO] DFAST_QC result json was written to GCF_006716765.1_ASM671676v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:17,650] [INFO] DFAST_QC completed!
[2024-01-24 10:50:17,650] [INFO] Total running time: 0h3m11s