[2024-01-24 12:22:37,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg6910adb4-d68f-4abf-8cd2-7fe47128f048/dqc_reference
[2024-01-24 12:22:39,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,336] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,336] [INFO] Running command: gunzip -c /var/lib/cwl/stga8f45e90-7400-459d-a6ec-92a3cff9277b/GCF_009908295.1_ASM990829v1_genomic.fna.gz | prodigal -d GCF_009908295.1_ASM990829v1_genomic.fna/cds.fna -a GCF_009908295.1_ASM990829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:03,827] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:03,828] [INFO] Task started: HMMsearch
[2024-01-24 12:23:03,828] [INFO] Running command: hmmsearch --tblout GCF_009908295.1_ASM990829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6910adb4-d68f-4abf-8cd2-7fe47128f048/dqc_reference/reference_markers.hmm GCF_009908295.1_ASM990829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:04,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:04,235] [INFO] Found 6/6 markers.
[2024-01-24 12:23:04,296] [INFO] Query marker FASTA was written to GCF_009908295.1_ASM990829v1_genomic.fna/markers.fasta
[2024-01-24 12:23:04,297] [INFO] Task started: Blastn
[2024-01-24 12:23:04,297] [INFO] Running command: blastn -query GCF_009908295.1_ASM990829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6910adb4-d68f-4abf-8cd2-7fe47128f048/dqc_reference/reference_markers.fasta -out GCF_009908295.1_ASM990829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:05,528] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:05,533] [INFO] Selected 21 target genomes.
[2024-01-24 12:23:05,534] [INFO] Target genome list was writen to GCF_009908295.1_ASM990829v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:05,543] [INFO] Task started: fastANI
[2024-01-24 12:23:05,544] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f45e90-7400-459d-a6ec-92a3cff9277b/GCF_009908295.1_ASM990829v1_genomic.fna.gz --refList GCF_009908295.1_ASM990829v1_genomic.fna/target_genomes.txt --output GCF_009908295.1_ASM990829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:46,642] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:46,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6910adb4-d68f-4abf-8cd2-7fe47128f048/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:46,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6910adb4-d68f-4abf-8cd2-7fe47128f048/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:46,671] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:46,671] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:46,672] [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
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	100.0	2473	2473	95	conclusive
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	88.3875	1599	2473	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	88.1883	1677	2473	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	88.1635	1654	2473	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	88.0888	1682	2473	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	87.0977	1393	2473	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	85.9164	1415	2473	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.8699	1073	2473	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	85.8654	1394	2473	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	85.7997	1355	2473	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	85.7461	1574	2473	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	85.7013	1447	2473	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	85.1457	1405	2473	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	84.8876	1465	2473	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.8668	1247	2473	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.3918	1267	2473	95	below_threshold
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	83.3918	1291	2473	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	83.336	1300	2473	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	76.4514	581	2473	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.3947	615	2473	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.2111	630	2473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:46,674] [INFO] DFAST Taxonomy check result was written to GCF_009908295.1_ASM990829v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:46,675] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:46,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:46,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6910adb4-d68f-4abf-8cd2-7fe47128f048/dqc_reference/checkm_data
[2024-01-24 12:23:46,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:46,746] [INFO] Task started: CheckM
[2024-01-24 12:23:46,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009908295.1_ASM990829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009908295.1_ASM990829v1_genomic.fna/checkm_input GCF_009908295.1_ASM990829v1_genomic.fna/checkm_result
[2024-01-24 12:25:08,847] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:08,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:08,874] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:08,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:08,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009908295.1_ASM990829v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:08,875] [INFO] Task started: Blastn
[2024-01-24 12:25:08,875] [INFO] Running command: blastn -query GCF_009908295.1_ASM990829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6910adb4-d68f-4abf-8cd2-7fe47128f048/dqc_reference/reference_markers_gtdb.fasta -out GCF_009908295.1_ASM990829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:10,674] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:10,678] [INFO] Selected 20 target genomes.
[2024-01-24 12:25:10,678] [INFO] Target genome list was writen to GCF_009908295.1_ASM990829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:10,691] [INFO] Task started: fastANI
[2024-01-24 12:25:10,692] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f45e90-7400-459d-a6ec-92a3cff9277b/GCF_009908295.1_ASM990829v1_genomic.fna.gz --refList GCF_009908295.1_ASM990829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009908295.1_ASM990829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:52,730] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:52,749] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:52,749] [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_009908295.1	s__Micromonospora rubida	100.0	2473	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003434305.1	s__Micromonospora sp003434305	92.7652	1734	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	88.3678	1601	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_000158815.1	s__Micromonospora sp000158815	88.21	1437	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.02	97.02	0.80	0.80	2	-
GCF_014205165.1	s__Micromonospora carbonacea	88.2087	1674	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_007830265.1	s__Micromonospora olivasterospora	87.0296	1400	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	85.8846	1426	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090285.1	s__Micromonospora inositola	85.874	1346	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	85.7806	1404	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	85.7225	1444	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_900091625.1	s__Micromonospora peucetia	85.6874	1582	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091445.1	s__Micromonospora echinofusca	85.5238	1507	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.23	97.23	0.90	0.90	2	-
GCF_900089595.1	s__Micromonospora auratinigra	85.4466	1443	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	85.3363	1308	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090305.1	s__Micromonospora siamensis	85.2032	1397	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091475.1	s__Micromonospora chersina	85.1654	1440	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_900089585.1	s__Micromonospora sediminicola	84.8739	1465	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.55	97.81	0.94	0.92	3	-
GCF_002926165.1	s__Micromonospora chalcea	84.8212	1418	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_003857055.1	s__Micromonospora inaquosa	84.0918	1286	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109115.1	s__Micromonospora phaseoli	83.4216	1288	2473	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:52,752] [INFO] GTDB search result was written to GCF_009908295.1_ASM990829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:52,753] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:52,757] [INFO] DFAST_QC result json was written to GCF_009908295.1_ASM990829v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:52,757] [INFO] DFAST_QC completed!
[2024-01-24 12:25:52,757] [INFO] Total running time: 0h3m15s