[2024-01-24 11:20:04,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,216] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbffd416-f5f3-4781-87f4-d38e33e7670d/dqc_reference
[2024-01-24 11:20:05,406] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,407] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,407] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c4169d9-2d48-4fb3-9032-96a93bbca806/GCF_015751785.1_ASM1575178v1_genomic.fna.gz | prodigal -d GCF_015751785.1_ASM1575178v1_genomic.fna/cds.fna -a GCF_015751785.1_ASM1575178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:26,449] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:26,450] [INFO] Task started: HMMsearch
[2024-01-24 11:20:26,450] [INFO] Running command: hmmsearch --tblout GCF_015751785.1_ASM1575178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbffd416-f5f3-4781-87f4-d38e33e7670d/dqc_reference/reference_markers.hmm GCF_015751785.1_ASM1575178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:26,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:26,729] [INFO] Found 6/6 markers.
[2024-01-24 11:20:26,781] [INFO] Query marker FASTA was written to GCF_015751785.1_ASM1575178v1_genomic.fna/markers.fasta
[2024-01-24 11:20:26,782] [INFO] Task started: Blastn
[2024-01-24 11:20:26,782] [INFO] Running command: blastn -query GCF_015751785.1_ASM1575178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbffd416-f5f3-4781-87f4-d38e33e7670d/dqc_reference/reference_markers.fasta -out GCF_015751785.1_ASM1575178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:27,908] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:27,911] [INFO] Selected 15 target genomes.
[2024-01-24 11:20:27,912] [INFO] Target genome list was writen to GCF_015751785.1_ASM1575178v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:27,916] [INFO] Task started: fastANI
[2024-01-24 11:20:27,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c4169d9-2d48-4fb3-9032-96a93bbca806/GCF_015751785.1_ASM1575178v1_genomic.fna.gz --refList GCF_015751785.1_ASM1575178v1_genomic.fna/target_genomes.txt --output GCF_015751785.1_ASM1575178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:54,621] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:54,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbffd416-f5f3-4781-87f4-d38e33e7670d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:54,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbffd416-f5f3-4781-87f4-d38e33e7670d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:54,635] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:54,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:54,635] [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 vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	100.0	2444	2446	95	conclusive
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	94.5258	2020	2446	95	below_threshold
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	94.4523	2092	2446	95	below_threshold
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	93.9399	1874	2446	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	93.7933	2005	2446	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	92.7355	1783	2446	95	below_threshold
Micromonospora violae	strain=DSM 45888	GCA_004217135.1	1278207	1278207	type	True	92.4217	1973	2446	95	below_threshold
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	90.8432	1878	2446	95	below_threshold
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	90.6551	1897	2446	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	90.5054	1890	2446	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	88.8646	1592	2446	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.3002	1156	2446	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.1023	1442	2446	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.9476	1462	2446	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.3095	1371	2446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:54,637] [INFO] DFAST Taxonomy check result was written to GCF_015751785.1_ASM1575178v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:54,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:54,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:54,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbffd416-f5f3-4781-87f4-d38e33e7670d/dqc_reference/checkm_data
[2024-01-24 11:20:54,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:54,705] [INFO] Task started: CheckM
[2024-01-24 11:20:54,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015751785.1_ASM1575178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015751785.1_ASM1575178v1_genomic.fna/checkm_input GCF_015751785.1_ASM1575178v1_genomic.fna/checkm_result
[2024-01-24 11:22:14,295] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:14,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:14,316] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:14,316] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:14,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015751785.1_ASM1575178v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:14,317] [INFO] Task started: Blastn
[2024-01-24 11:22:14,317] [INFO] Running command: blastn -query GCF_015751785.1_ASM1575178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbffd416-f5f3-4781-87f4-d38e33e7670d/dqc_reference/reference_markers_gtdb.fasta -out GCF_015751785.1_ASM1575178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:16,042] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:16,045] [INFO] Selected 9 target genomes.
[2024-01-24 11:22:16,045] [INFO] Target genome list was writen to GCF_015751785.1_ASM1575178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:16,050] [INFO] Task started: fastANI
[2024-01-24 11:22:16,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c4169d9-2d48-4fb3-9032-96a93bbca806/GCF_015751785.1_ASM1575178v1_genomic.fna.gz --refList GCF_015751785.1_ASM1575178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015751785.1_ASM1575178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:33,415] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:33,423] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:33,424] [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_015751785.1	s__Micromonospora vinacea	100.0	2444	2446	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_003264365.1	s__Micromonospora noduli	94.5258	2020	2446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.92	97.90	0.94	0.91	8	-
GCF_900091575.1	s__Micromonospora saelicesensis	94.4523	2092	2446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_018070325.1	s__Micromonospora sp018070325	94.2406	1966	2446	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	93.9398	1873	2446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.1103	N/A	N/A	N/A	N/A	1	-
GCF_015751765.1	s__Micromonospora ureilytica	93.8083	2003	2446	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	92.7456	1782	2446	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	92.4258	1973	2446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205615.1	s__Micromonospora arborensis	90.3081	1834	2446	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 11:22:33,426] [INFO] GTDB search result was written to GCF_015751785.1_ASM1575178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:33,426] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:33,429] [INFO] DFAST_QC result json was written to GCF_015751785.1_ASM1575178v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:33,429] [INFO] DFAST_QC completed!
[2024-01-24 11:22:33,429] [INFO] Total running time: 0h2m29s