[2024-01-24 13:31:32,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:32,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:32,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg6354e845-9cac-4431-ab6a-100eb7129361/dqc_reference
[2024-01-24 13:31:33,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:33,305] [INFO] Task started: Prodigal
[2024-01-24 13:31:33,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f972b6d-4b9d-410e-b4f5-3b9284bdb040/GCF_015690345.1_ASM1569034v1_genomic.fna.gz | prodigal -d GCF_015690345.1_ASM1569034v1_genomic.fna/cds.fna -a GCF_015690345.1_ASM1569034v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:58,372] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:58,372] [INFO] Task started: HMMsearch
[2024-01-24 13:31:58,372] [INFO] Running command: hmmsearch --tblout GCF_015690345.1_ASM1569034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6354e845-9cac-4431-ab6a-100eb7129361/dqc_reference/reference_markers.hmm GCF_015690345.1_ASM1569034v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:58,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:58,791] [INFO] Found 6/6 markers.
[2024-01-24 13:31:58,870] [INFO] Query marker FASTA was written to GCF_015690345.1_ASM1569034v1_genomic.fna/markers.fasta
[2024-01-24 13:31:58,871] [INFO] Task started: Blastn
[2024-01-24 13:31:58,871] [INFO] Running command: blastn -query GCF_015690345.1_ASM1569034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6354e845-9cac-4431-ab6a-100eb7129361/dqc_reference/reference_markers.fasta -out GCF_015690345.1_ASM1569034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:00,039] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:00,049] [INFO] Selected 36 target genomes.
[2024-01-24 13:32:00,050] [INFO] Target genome list was writen to GCF_015690345.1_ASM1569034v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:00,070] [INFO] Task started: fastANI
[2024-01-24 13:32:00,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f972b6d-4b9d-410e-b4f5-3b9284bdb040/GCF_015690345.1_ASM1569034v1_genomic.fna.gz --refList GCF_015690345.1_ASM1569034v1_genomic.fna/target_genomes.txt --output GCF_015690345.1_ASM1569034v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:53,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:53,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6354e845-9cac-4431-ab6a-100eb7129361/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:53,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6354e845-9cac-4431-ab6a-100eb7129361/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:53,238] [INFO] Found 36 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:53,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:53,238] [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 phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	81.1572	917	2854	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	80.8375	977	2854	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	80.7791	1175	2854	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	80.6882	1149	2854	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	80.6795	1106	2854	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	80.6571	1139	2854	95	below_threshold
Micromonospora inyonensis	strain=DSM 46123	GCA_900091415.1	47866	47866	type	True	80.5801	1006	2854	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	80.5748	1198	2854	95	below_threshold
Micromonospora cremea	strain=DSM 45599	GCA_900143515.1	709881	709881	type	True	80.554	1195	2854	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	80.5525	1024	2854	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	80.5375	1123	2854	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	80.5162	1062	2854	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	80.5062	1115	2854	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	80.4874	1115	2854	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	80.4848	1204	2854	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	80.4518	1190	2854	95	below_threshold
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	80.4025	1158	2854	95	below_threshold
Micromonospora violae	strain=DSM 45888	GCA_004217135.1	1278207	1278207	type	True	80.3773	1189	2854	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	80.3727	1202	2854	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	80.3676	1050	2854	95	below_threshold
Micromonospora pallida	strain=DSM 43817	GCA_900090325.1	145854	145854	type	True	80.3616	1116	2854	95	below_threshold
Micromonospora yangpuensis	strain=CGMCC 4.5736	GCA_014645775.1	683228	683228	type	True	80.357	1062	2854	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	80.3308	1203	2854	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	80.314	1162	2854	95	below_threshold
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	80.3062	1073	2854	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	80.2769	1119	2854	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	80.2631	1081	2854	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	80.2556	1160	2854	95	below_threshold
Micromonospora taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	80.229	1182	2854	95	below_threshold
Micromonospora musae	strain=MS1-9	GCA_003626635.1	1894970	1894970	type	True	80.1677	1154	2854	95	below_threshold
Micromonospora chokoriensis	strain=DSM 45160	GCA_900091505.1	356851	356851	type	True	80.1647	1176	2854	95	below_threshold
Salinispora mooreana	strain=CNT-150	GCA_000514435.1	999545	999545	type	True	79.2862	702	2854	95	below_threshold
Salinispora mooreana	strain=DSM 45549	GCA_000379065.1	999545	999545	type	True	79.2434	713	2854	95	below_threshold
Salinispora arenicola	strain=DSM 44819	GCA_006716065.1	168697	168697	type	True	79.0764	740	2854	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	78.3281	1079	2854	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	78.0409	1015	2854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:53,240] [INFO] DFAST Taxonomy check result was written to GCF_015690345.1_ASM1569034v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:53,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:53,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:53,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6354e845-9cac-4431-ab6a-100eb7129361/dqc_reference/checkm_data
[2024-01-24 13:32:53,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:53,330] [INFO] Task started: CheckM
[2024-01-24 13:32:53,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015690345.1_ASM1569034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015690345.1_ASM1569034v1_genomic.fna/checkm_input GCF_015690345.1_ASM1569034v1_genomic.fna/checkm_result
[2024-01-24 13:34:04,108] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:04,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:04,137] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:04,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:04,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015690345.1_ASM1569034v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:04,138] [INFO] Task started: Blastn
[2024-01-24 13:34:04,138] [INFO] Running command: blastn -query GCF_015690345.1_ASM1569034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6354e845-9cac-4431-ab6a-100eb7129361/dqc_reference/reference_markers_gtdb.fasta -out GCF_015690345.1_ASM1569034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:05,892] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:05,897] [INFO] Selected 17 target genomes.
[2024-01-24 13:34:05,897] [INFO] Target genome list was writen to GCF_015690345.1_ASM1569034v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:05,913] [INFO] Task started: fastANI
[2024-01-24 13:34:05,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f972b6d-4b9d-410e-b4f5-3b9284bdb040/GCF_015690345.1_ASM1569034v1_genomic.fna.gz --refList GCF_015690345.1_ASM1569034v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015690345.1_ASM1569034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:38,363] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:38,385] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:38,385] [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_015690345.1	s__Plantactinospora sp015690345	100.0	2828	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014874095.1	s__Plantactinospora soyae	90.3022	2059	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030345.1	s__Plantactinospora sp003030345	85.4373	1773	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_016862915.1	s__Plantactinospora endophytica	85.2515	1830	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862935.1	s__Plantactinospora mayteni	85.2447	1785	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846275.1	s__Plantactinospora sp002846275	84.9245	1679	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217235.1	s__Plantactinospora sp004217235	84.7758	1590	2854	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	82.7999	1337	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633685.1	s__Micromonospora_G pisi	81.0627	1337	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003434305.1	s__Micromonospora sp003434305	80.7301	1113	2854	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	80.6809	1105	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091415.1	s__Micromonospora inyonensis	80.5814	1007	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.10	96.06	0.74	0.74	3	-
GCF_900143515.1	s__Micromonospora cremea	80.5808	1188	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017614955.1	s__Micromonospora echinofusca_A	80.465	1056	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712475.1	s__Micromonospora sp009712475	80.0979	1031	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721075.1	s__Streptosporangium amethystogenes	76.3947	588	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024865.1	s__Streptosporangium roseum	76.384	702	2854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:38,387] [INFO] GTDB search result was written to GCF_015690345.1_ASM1569034v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:38,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:38,392] [INFO] DFAST_QC result json was written to GCF_015690345.1_ASM1569034v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:38,392] [INFO] DFAST_QC completed!
[2024-01-24 13:34:38,392] [INFO] Total running time: 0h3m6s