[2024-01-24 11:19:55,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg87dc2bf4-9696-4418-9225-24bd5763f72a/dqc_reference
[2024-01-24 11:19:56,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,484] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,484] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c218a13-3975-4ff0-a4ef-250547831e10/GCF_022230925.1_ASM2223092v1_genomic.fna.gz | prodigal -d GCF_022230925.1_ASM2223092v1_genomic.fna/cds.fna -a GCF_022230925.1_ASM2223092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:18,421] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:18,421] [INFO] Task started: HMMsearch
[2024-01-24 11:20:18,421] [INFO] Running command: hmmsearch --tblout GCF_022230925.1_ASM2223092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87dc2bf4-9696-4418-9225-24bd5763f72a/dqc_reference/reference_markers.hmm GCF_022230925.1_ASM2223092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:18,755] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:18,756] [INFO] Found 6/6 markers.
[2024-01-24 11:20:18,824] [INFO] Query marker FASTA was written to GCF_022230925.1_ASM2223092v1_genomic.fna/markers.fasta
[2024-01-24 11:20:18,824] [INFO] Task started: Blastn
[2024-01-24 11:20:18,824] [INFO] Running command: blastn -query GCF_022230925.1_ASM2223092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87dc2bf4-9696-4418-9225-24bd5763f72a/dqc_reference/reference_markers.fasta -out GCF_022230925.1_ASM2223092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:20,085] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:20,089] [INFO] Selected 20 target genomes.
[2024-01-24 11:20:20,089] [INFO] Target genome list was writen to GCF_022230925.1_ASM2223092v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:20,099] [INFO] Task started: fastANI
[2024-01-24 11:20:20,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c218a13-3975-4ff0-a4ef-250547831e10/GCF_022230925.1_ASM2223092v1_genomic.fna.gz --refList GCF_022230925.1_ASM2223092v1_genomic.fna/target_genomes.txt --output GCF_022230925.1_ASM2223092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:56,537] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:56,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87dc2bf4-9696-4418-9225-24bd5763f72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:56,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87dc2bf4-9696-4418-9225-24bd5763f72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:56,558] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:56,558] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:20:56,558] [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 saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	95.0748	2077	2488	95	inconclusive
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	95.0659	2002	2488	95	inconclusive
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	94.6992	1849	2488	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	93.8215	2062	2488	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	93.4993	1966	2488	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	92.7485	1811	2488	95	below_threshold
Micromonospora violae	strain=DSM 45888	GCA_004217135.1	1278207	1278207	type	True	92.2153	1940	2488	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	90.1322	1806	2488	95	below_threshold
Micromonospora parathelypteridis	strain=CGMCC 4.7347	GCA_014646315.1	1839617	1839617	type	True	90.1296	1803	2488	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	89.974	1821	2488	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	88.5511	1554	2488	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.0805	1131	2488	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	84.5055	1198	2488	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	84.372	1441	2488	95	below_threshold
Micromonospora endolithica	strain=DSM 44398	GCA_007994185.1	230091	230091	type	True	84.1999	1515	2488	95	below_threshold
Micromonospora endolithica	strain=JCM 12677	GCA_003626595.1	230091	230091	type	True	84.1987	1507	2488	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.731	1429	2488	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.666	1474	2488	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.1536	1338	2488	95	below_threshold
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	78.0412	895	2488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:56,565] [INFO] DFAST Taxonomy check result was written to GCF_022230925.1_ASM2223092v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:56,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:56,566] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:56,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87dc2bf4-9696-4418-9225-24bd5763f72a/dqc_reference/checkm_data
[2024-01-24 11:20:56,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:56,646] [INFO] Task started: CheckM
[2024-01-24 11:20:56,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022230925.1_ASM2223092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022230925.1_ASM2223092v1_genomic.fna/checkm_input GCF_022230925.1_ASM2223092v1_genomic.fna/checkm_result
[2024-01-24 11:22:07,493] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:07,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:07,520] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:07,521] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:07,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022230925.1_ASM2223092v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:07,521] [INFO] Task started: Blastn
[2024-01-24 11:22:07,522] [INFO] Running command: blastn -query GCF_022230925.1_ASM2223092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87dc2bf4-9696-4418-9225-24bd5763f72a/dqc_reference/reference_markers_gtdb.fasta -out GCF_022230925.1_ASM2223092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:09,390] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:09,395] [INFO] Selected 16 target genomes.
[2024-01-24 11:22:09,395] [INFO] Target genome list was writen to GCF_022230925.1_ASM2223092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:09,407] [INFO] Task started: fastANI
[2024-01-24 11:22:09,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c218a13-3975-4ff0-a4ef-250547831e10/GCF_022230925.1_ASM2223092v1_genomic.fna.gz --refList GCF_022230925.1_ASM2223092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022230925.1_ASM2223092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:39,476] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:39,495] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:22:39,495] [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_900091575.1	s__Micromonospora saelicesensis	95.0677	2078	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_003264365.1	s__Micromonospora noduli	95.0551	2003	2488	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	94.9554	1940	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_003857035.1	s__Micromonospora arida	94.6992	1849	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.1103	N/A	N/A	N/A	N/A	1	-
GCF_015751785.1	s__Micromonospora vinacea	93.8215	2062	2488	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	93.4896	1967	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	97.34	0.88	0.87	3	-
GCF_003857055.1	s__Micromonospora inaquosa	92.7469	1812	2488	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	92.2064	1941	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718555.1	s__Micromonospora chokoriensis_B	92.0551	1817	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201145.1	s__Micromonospora parathelypteridis	90.1326	1806	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907275.1	s__Micromonospora luteifusca	89.9709	1822	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236335.1	s__Micromonospora deserti	84.5699	1190	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	84.3738	1441	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	83.4643	1427	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364215.1	s__Micromonospora sp004307965	82.7801	1370	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_016862975.1	s__Rugosimonospora africana	78.0135	902	2488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:39,497] [INFO] GTDB search result was written to GCF_022230925.1_ASM2223092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:39,498] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:39,506] [INFO] DFAST_QC result json was written to GCF_022230925.1_ASM2223092v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:39,506] [INFO] DFAST_QC completed!
[2024-01-24 11:22:39,506] [INFO] Total running time: 0h2m44s