[2024-01-25 19:59:35,437] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:35,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:35,438] [INFO] DQC Reference Directory: /var/lib/cwl/stge37da6f0-45b1-4766-9139-6758421d3315/dqc_reference
[2024-01-25 19:59:36,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:36,722] [INFO] Task started: Prodigal
[2024-01-25 19:59:36,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2bf01b1-a6e2-4f4e-b47b-8fab2a09eeb0/GCF_003172955.1_ASM317295v1_genomic.fna.gz | prodigal -d GCF_003172955.1_ASM317295v1_genomic.fna/cds.fna -a GCF_003172955.1_ASM317295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:51,969] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:51,969] [INFO] Task started: HMMsearch
[2024-01-25 19:59:51,969] [INFO] Running command: hmmsearch --tblout GCF_003172955.1_ASM317295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge37da6f0-45b1-4766-9139-6758421d3315/dqc_reference/reference_markers.hmm GCF_003172955.1_ASM317295v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:52,264] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:52,265] [INFO] Found 6/6 markers.
[2024-01-25 19:59:52,317] [INFO] Query marker FASTA was written to GCF_003172955.1_ASM317295v1_genomic.fna/markers.fasta
[2024-01-25 19:59:52,317] [INFO] Task started: Blastn
[2024-01-25 19:59:52,317] [INFO] Running command: blastn -query GCF_003172955.1_ASM317295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge37da6f0-45b1-4766-9139-6758421d3315/dqc_reference/reference_markers.fasta -out GCF_003172955.1_ASM317295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:53,394] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:53,397] [INFO] Selected 16 target genomes.
[2024-01-25 19:59:53,398] [INFO] Target genome list was writen to GCF_003172955.1_ASM317295v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:53,415] [INFO] Task started: fastANI
[2024-01-25 19:59:53,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2bf01b1-a6e2-4f4e-b47b-8fab2a09eeb0/GCF_003172955.1_ASM317295v1_genomic.fna.gz --refList GCF_003172955.1_ASM317295v1_genomic.fna/target_genomes.txt --output GCF_003172955.1_ASM317295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:22,001] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:22,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge37da6f0-45b1-4766-9139-6758421d3315/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:22,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge37da6f0-45b1-4766-9139-6758421d3315/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:22,012] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:22,013] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:22,013] [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 acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	100.0	1959	1976	95	conclusive
Micromonospora cremea	strain=DSM 45599	GCA_900143515.1	709881	709881	type	True	92.068	1600	1976	95	below_threshold
Micromonospora coriariae	strain=DSM 44875	GCA_900091455.1	285665	285665	type	True	91.5746	1604	1976	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	89.4813	1404	1976	95	below_threshold
Micromonospora parathelypteridis	strain=CGMCC 4.7347	GCA_014646315.1	1839617	1839617	type	True	89.2613	1554	1976	95	below_threshold
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	89.2327	1562	1976	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	89.2083	1574	1976	95	below_threshold
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	89.0812	1581	1976	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	88.9449	1537	1976	95	below_threshold
Micromonospora arida	strain=LB32	GCA_003857035.1	2203715	2203715	type	True	88.7616	1481	1976	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	88.7363	1509	1976	95	below_threshold
Micromonospora profundi	strain=DSM 45981	GCA_011927785.1	1420889	1420889	type	True	88.268	1428	1976	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	86.4962	1068	1976	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.6624	1286	1976	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.4385	1275	1976	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.8135	1181	1976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:22,016] [INFO] DFAST Taxonomy check result was written to GCF_003172955.1_ASM317295v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:22,017] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:22,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:22,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge37da6f0-45b1-4766-9139-6758421d3315/dqc_reference/checkm_data
[2024-01-25 20:00:22,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:22,077] [INFO] Task started: CheckM
[2024-01-25 20:00:22,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003172955.1_ASM317295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003172955.1_ASM317295v1_genomic.fna/checkm_input GCF_003172955.1_ASM317295v1_genomic.fna/checkm_result
[2024-01-25 20:01:20,179] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:20,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:20,209] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:20,210] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:20,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003172955.1_ASM317295v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:20,210] [INFO] Task started: Blastn
[2024-01-25 20:01:20,210] [INFO] Running command: blastn -query GCF_003172955.1_ASM317295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge37da6f0-45b1-4766-9139-6758421d3315/dqc_reference/reference_markers_gtdb.fasta -out GCF_003172955.1_ASM317295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:21,906] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:21,908] [INFO] Selected 11 target genomes.
[2024-01-25 20:01:21,908] [INFO] Target genome list was writen to GCF_003172955.1_ASM317295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:21,941] [INFO] Task started: fastANI
[2024-01-25 20:01:21,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2bf01b1-a6e2-4f4e-b47b-8fab2a09eeb0/GCF_003172955.1_ASM317295v1_genomic.fna.gz --refList GCF_003172955.1_ASM317295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003172955.1_ASM317295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:42,321] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:42,329] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:42,330] [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_003172955.1	s__Micromonospora sp003172955	100.0	1958	1976	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_900143515.1	s__Micromonospora cremea	92.0898	1598	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070045.1	s__Micromonospora sp018070045	91.9838	1631	1976	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	91.8739	1571	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_900091455.1	s__Micromonospora coriariae	91.578	1603	1976	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	89.9878	1385	1976	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	89.2056	1574	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003205615.1	s__Micromonospora arborensis	89.0152	1460	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070325.1	s__Micromonospora sp018070325	88.9025	1497	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_000718515.1	s__Micromonospora parva	88.8277	1520	1976	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	88.6857	1436	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:42,331] [INFO] GTDB search result was written to GCF_003172955.1_ASM317295v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:42,332] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:42,335] [INFO] DFAST_QC result json was written to GCF_003172955.1_ASM317295v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:42,335] [INFO] DFAST_QC completed!
[2024-01-25 20:01:42,336] [INFO] Total running time: 0h2m7s