[2024-01-24 11:20:19,325] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,328] [INFO] DQC Reference Directory: /var/lib/cwl/stga9a9cb7b-2b1f-42b7-ae71-53216136219f/dqc_reference
[2024-01-24 11:20:20,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,541] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,541] [INFO] Running command: gunzip -c /var/lib/cwl/stg9882bb96-a1cd-4e40-8f48-e326457c7040/GCF_013410645.1_ASM1341064v1_genomic.fna.gz | prodigal -d GCF_013410645.1_ASM1341064v1_genomic.fna/cds.fna -a GCF_013410645.1_ASM1341064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:40,689] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:40,690] [INFO] Task started: HMMsearch
[2024-01-24 11:20:40,690] [INFO] Running command: hmmsearch --tblout GCF_013410645.1_ASM1341064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9a9cb7b-2b1f-42b7-ae71-53216136219f/dqc_reference/reference_markers.hmm GCF_013410645.1_ASM1341064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:41,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:41,104] [INFO] Found 6/6 markers.
[2024-01-24 11:20:41,158] [INFO] Query marker FASTA was written to GCF_013410645.1_ASM1341064v1_genomic.fna/markers.fasta
[2024-01-24 11:20:41,158] [INFO] Task started: Blastn
[2024-01-24 11:20:41,158] [INFO] Running command: blastn -query GCF_013410645.1_ASM1341064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9a9cb7b-2b1f-42b7-ae71-53216136219f/dqc_reference/reference_markers.fasta -out GCF_013410645.1_ASM1341064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:42,304] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:42,308] [INFO] Selected 17 target genomes.
[2024-01-24 11:20:42,308] [INFO] Target genome list was writen to GCF_013410645.1_ASM1341064v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:42,316] [INFO] Task started: fastANI
[2024-01-24 11:20:42,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg9882bb96-a1cd-4e40-8f48-e326457c7040/GCF_013410645.1_ASM1341064v1_genomic.fna.gz --refList GCF_013410645.1_ASM1341064v1_genomic.fna/target_genomes.txt --output GCF_013410645.1_ASM1341064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:13,722] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:13,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9a9cb7b-2b1f-42b7-ae71-53216136219f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:13,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9a9cb7b-2b1f-42b7-ae71-53216136219f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:13,739] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:21:13,739] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:21:13,740] [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 jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	100.0	2275	2275	95	inconclusive
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	96.315	2057	2275	95	inconclusive
Micromonospora taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	91.1406	1918	2275	95	below_threshold
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	91.1231	1866	2275	95	below_threshold
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	90.9764	1809	2275	95	below_threshold
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	90.9735	1745	2275	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	90.8343	1887	2275	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	90.8209	1784	2275	95	below_threshold
Micromonospora chokoriensis	strain=DSM 45160	GCA_900091505.1	356851	356851	type	True	90.7288	1837	2275	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	90.6506	1778	2275	95	below_threshold
Micromonospora violae	strain=DSM 45888	GCA_004217135.1	1278207	1278207	type	True	90.3483	1785	2275	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	89.5654	1584	2275	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	89.2881	1535	2275	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.5859	1101	2275	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.0316	1415	2275	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.9982	1464	2275	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.3344	1347	2275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:13,741] [INFO] DFAST Taxonomy check result was written to GCF_013410645.1_ASM1341064v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:13,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:13,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:13,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9a9cb7b-2b1f-42b7-ae71-53216136219f/dqc_reference/checkm_data
[2024-01-24 11:21:13,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:13,803] [INFO] Task started: CheckM
[2024-01-24 11:21:13,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410645.1_ASM1341064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410645.1_ASM1341064v1_genomic.fna/checkm_input GCF_013410645.1_ASM1341064v1_genomic.fna/checkm_result
[2024-01-24 11:22:32,416] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:32,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:32,444] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:32,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:32,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410645.1_ASM1341064v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:32,445] [INFO] Task started: Blastn
[2024-01-24 11:22:32,445] [INFO] Running command: blastn -query GCF_013410645.1_ASM1341064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9a9cb7b-2b1f-42b7-ae71-53216136219f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410645.1_ASM1341064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:34,162] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:34,167] [INFO] Selected 16 target genomes.
[2024-01-24 11:22:34,167] [INFO] Target genome list was writen to GCF_013410645.1_ASM1341064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:34,180] [INFO] Task started: fastANI
[2024-01-24 11:22:34,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg9882bb96-a1cd-4e40-8f48-e326457c7040/GCF_013410645.1_ASM1341064v1_genomic.fna.gz --refList GCF_013410645.1_ASM1341064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410645.1_ASM1341064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:02,811] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:02,829] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:02,829] [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_900090275.1	s__Micromonospora zamorensis	96.3075	2060	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.71	96.30	0.91	0.89	6	conclusive
GCF_900091575.1	s__Micromonospora saelicesensis	91.119	1867	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_003857035.1	s__Micromonospora arida	91.0027	1741	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.1103	N/A	N/A	N/A	N/A	1	-
GCF_003264365.1	s__Micromonospora noduli	90.9937	1806	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.92	97.90	0.94	0.91	8	-
GCF_018070325.1	s__Micromonospora sp018070325	90.8387	1758	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_015751785.1	s__Micromonospora vinacea	90.7919	1893	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751765.1	s__Micromonospora ureilytica	90.7885	1787	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	97.34	0.88	0.87	3	-
GCF_900091505.1	s__Micromonospora chokoriensis	90.7247	1839	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.10	95.10	0.89	0.89	2	-
GCF_014201145.1	s__Micromonospora parathelypteridis	90.6491	1795	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000718515.1	s__Micromonospora parva	90.6249	1850	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.24	99.24	0.97	0.97	2	-
GCF_003857055.1	s__Micromonospora inaquosa	90.4304	1645	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217135.1	s__Micromonospora violae	90.3393	1786	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803395.1	s__Micromonospora sp016803395	89.9086	1548	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016802865.1	s__Micromonospora sp016802865	89.5711	1490	2275	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	89.5422	1586	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297395.2	s__Micromonospora lupini	88.925	1804	2275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:02,830] [INFO] GTDB search result was written to GCF_013410645.1_ASM1341064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:02,831] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:02,835] [INFO] DFAST_QC result json was written to GCF_013410645.1_ASM1341064v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:02,835] [INFO] DFAST_QC completed!
[2024-01-24 11:23:02,835] [INFO] Total running time: 0h2m44s