[2024-01-24 13:23:11,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:11,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:11,590] [INFO] DQC Reference Directory: /var/lib/cwl/stgfca82930-4823-4764-8965-f96034fd2b8c/dqc_reference
[2024-01-24 13:23:13,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:13,026] [INFO] Task started: Prodigal
[2024-01-24 13:23:13,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg16fffc66-5e6e-4240-adc3-c8ff58c1aa6a/GCF_007830265.1_ASM783026v1_genomic.fna.gz | prodigal -d GCF_007830265.1_ASM783026v1_genomic.fna/cds.fna -a GCF_007830265.1_ASM783026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:51,367] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:51,368] [INFO] Task started: HMMsearch
[2024-01-24 13:23:51,368] [INFO] Running command: hmmsearch --tblout GCF_007830265.1_ASM783026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfca82930-4823-4764-8965-f96034fd2b8c/dqc_reference/reference_markers.hmm GCF_007830265.1_ASM783026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:51,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:51,686] [INFO] Found 6/6 markers.
[2024-01-24 13:23:51,748] [INFO] Query marker FASTA was written to GCF_007830265.1_ASM783026v1_genomic.fna/markers.fasta
[2024-01-24 13:23:51,749] [INFO] Task started: Blastn
[2024-01-24 13:23:51,749] [INFO] Running command: blastn -query GCF_007830265.1_ASM783026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfca82930-4823-4764-8965-f96034fd2b8c/dqc_reference/reference_markers.fasta -out GCF_007830265.1_ASM783026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:52,951] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:52,956] [INFO] Selected 26 target genomes.
[2024-01-24 13:23:52,956] [INFO] Target genome list was writen to GCF_007830265.1_ASM783026v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:53,003] [INFO] Task started: fastANI
[2024-01-24 13:23:53,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg16fffc66-5e6e-4240-adc3-c8ff58c1aa6a/GCF_007830265.1_ASM783026v1_genomic.fna.gz --refList GCF_007830265.1_ASM783026v1_genomic.fna/target_genomes.txt --output GCF_007830265.1_ASM783026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:41,086] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:41,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfca82930-4823-4764-8965-f96034fd2b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:41,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfca82930-4823-4764-8965-f96034fd2b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:41,112] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:41,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:41,112] [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 olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	100.0	2355	2357	95	conclusive
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	87.1061	1409	2357	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	87.0104	1408	2357	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	86.9689	1414	2357	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	86.7327	1414	2357	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	85.9915	1352	2357	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	85.8362	1352	2357	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	85.7157	1264	2357	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	85.7088	1328	2357	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	85.6833	1362	2357	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	85.5978	1327	2357	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	85.5005	1047	2357	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	85.491	1329	2357	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	85.4437	1357	2357	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	85.4252	1276	2357	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.2932	1045	2357	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	85.1683	1326	2357	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.8293	1305	2357	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.6948	1170	2357	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.6431	1291	2357	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	84.2723	1219	2357	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	84.2214	1220	2357	95	below_threshold
Micromonospora avicenniae	strain=DSM 45758	GCA_900156065.1	1198245	1198245	type	True	83.7705	1253	2357	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.4178	1176	2357	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	83.3021	1197	2357	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	83.2461	1195	2357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:41,114] [INFO] DFAST Taxonomy check result was written to GCF_007830265.1_ASM783026v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:41,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:41,115] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:41,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfca82930-4823-4764-8965-f96034fd2b8c/dqc_reference/checkm_data
[2024-01-24 13:24:41,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:41,181] [INFO] Task started: CheckM
[2024-01-24 13:24:41,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830265.1_ASM783026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830265.1_ASM783026v1_genomic.fna/checkm_input GCF_007830265.1_ASM783026v1_genomic.fna/checkm_result
[2024-01-24 13:26:36,380] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:36,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:36,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:36,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:36,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830265.1_ASM783026v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:36,406] [INFO] Task started: Blastn
[2024-01-24 13:26:36,406] [INFO] Running command: blastn -query GCF_007830265.1_ASM783026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfca82930-4823-4764-8965-f96034fd2b8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830265.1_ASM783026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:38,317] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:38,321] [INFO] Selected 23 target genomes.
[2024-01-24 13:26:38,322] [INFO] Target genome list was writen to GCF_007830265.1_ASM783026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:38,348] [INFO] Task started: fastANI
[2024-01-24 13:26:38,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg16fffc66-5e6e-4240-adc3-c8ff58c1aa6a/GCF_007830265.1_ASM783026v1_genomic.fna.gz --refList GCF_007830265.1_ASM783026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830265.1_ASM783026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:21,654] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:21,678] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:21,679] [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_007830265.1	s__Micromonospora olivasterospora	100.0	2354	2357	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	87.8878	1443	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	87.0796	1400	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_009908295.1	s__Micromonospora rubida	87.0049	1397	2357	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	86.9769	1414	2357	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	86.8486	1326	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.02	97.02	0.80	0.80	2	-
GCF_004217615.1	s__Micromonospora kangleipakensis	85.9894	1350	2357	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	85.8183	1350	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_014648395.1	s__Micromonospora fulviviridis	85.6492	1366	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_003725545.1	s__Micromonospora sp003725545	85.5255	1197	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_003857015.1	s__Micromonospora globispora	85.502	1046	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.52	99.52	0.89	0.89	2	-
GCF_900090245.1	s__Micromonospora halophytica	85.4249	1275	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664255.1	s__Micromonospora sp003664255	85.2374	1352	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090225.1	s__Micromonospora eburnea	85.1459	1327	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667505.1	s__Micromonospora sp003667505	84.7155	1211	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_003027925.1	s__Micromonospora sp003027925	84.6476	1298	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567585.1	s__Micromonospora rosaria	84.2942	1216	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228125.1	s__Micromonospora orduensis	84.1965	1222	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751785.1	s__Micromonospora vinacea	83.9065	1293	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156065.1	s__Micromonospora avicenniae	83.7321	1258	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070465.1	s__Micromonospora sp018070465	83.1841	1150	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217235.1	s__Plantactinospora sp004217235	81.0971	1129	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762835.1	s__Plantactinospora sp003762835	80.8956	1023	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:21,681] [INFO] GTDB search result was written to GCF_007830265.1_ASM783026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:21,682] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:21,692] [INFO] DFAST_QC result json was written to GCF_007830265.1_ASM783026v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:21,692] [INFO] DFAST_QC completed!
[2024-01-24 13:27:21,693] [INFO] Total running time: 0h4m10s