[2024-01-24 12:05:26,608] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgaae83832-c979-4b1a-a093-40cbcb9b7b36/dqc_reference
[2024-01-24 12:05:30,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,678] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,678] [INFO] Running command: gunzip -c /var/lib/cwl/stga5122545-6a4e-451d-801d-0e72f55885b0/GCF_025137375.1_ASM2513737v1_genomic.fna.gz | prodigal -d GCF_025137375.1_ASM2513737v1_genomic.fna/cds.fna -a GCF_025137375.1_ASM2513737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:10,325] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:10,325] [INFO] Task started: HMMsearch
[2024-01-24 12:06:10,326] [INFO] Running command: hmmsearch --tblout GCF_025137375.1_ASM2513737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaae83832-c979-4b1a-a093-40cbcb9b7b36/dqc_reference/reference_markers.hmm GCF_025137375.1_ASM2513737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:10,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:10,773] [INFO] Found 6/6 markers.
[2024-01-24 12:06:10,856] [INFO] Query marker FASTA was written to GCF_025137375.1_ASM2513737v1_genomic.fna/markers.fasta
[2024-01-24 12:06:10,857] [INFO] Task started: Blastn
[2024-01-24 12:06:10,857] [INFO] Running command: blastn -query GCF_025137375.1_ASM2513737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae83832-c979-4b1a-a093-40cbcb9b7b36/dqc_reference/reference_markers.fasta -out GCF_025137375.1_ASM2513737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:12,182] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:12,186] [INFO] Selected 10 target genomes.
[2024-01-24 12:06:12,187] [INFO] Target genome list was writen to GCF_025137375.1_ASM2513737v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:12,192] [INFO] Task started: fastANI
[2024-01-24 12:06:12,193] [INFO] Running command: fastANI --query /var/lib/cwl/stga5122545-6a4e-451d-801d-0e72f55885b0/GCF_025137375.1_ASM2513737v1_genomic.fna.gz --refList GCF_025137375.1_ASM2513737v1_genomic.fna/target_genomes.txt --output GCF_025137375.1_ASM2513737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:42,005] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:42,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaae83832-c979-4b1a-a093-40cbcb9b7b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:42,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaae83832-c979-4b1a-a093-40cbcb9b7b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:42,016] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:42,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:42,016] [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
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	100.0	3498	3498	95	conclusive
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	92.8186	1947	3498	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	85.0752	2225	3498	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	82.6589	2046	3498	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	82.5272	2038	3498	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	82.5143	2030	3498	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	81.727	1818	3498	95	below_threshold
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	81.6215	1890	3498	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.3204	946	3498	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	77.8634	1059	3498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:42,018] [INFO] DFAST Taxonomy check result was written to GCF_025137375.1_ASM2513737v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:42,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:42,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:42,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaae83832-c979-4b1a-a093-40cbcb9b7b36/dqc_reference/checkm_data
[2024-01-24 12:06:42,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:42,117] [INFO] Task started: CheckM
[2024-01-24 12:06:42,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025137375.1_ASM2513737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025137375.1_ASM2513737v1_genomic.fna/checkm_input GCF_025137375.1_ASM2513737v1_genomic.fna/checkm_result
[2024-01-24 12:09:45,936] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:45,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.42%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:45,974] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:45,974] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:45,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025137375.1_ASM2513737v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:45,975] [INFO] Task started: Blastn
[2024-01-24 12:09:45,975] [INFO] Running command: blastn -query GCF_025137375.1_ASM2513737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae83832-c979-4b1a-a093-40cbcb9b7b36/dqc_reference/reference_markers_gtdb.fasta -out GCF_025137375.1_ASM2513737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:47,952] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:47,960] [INFO] Selected 15 target genomes.
[2024-01-24 12:09:47,961] [INFO] Target genome list was writen to GCF_025137375.1_ASM2513737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:47,972] [INFO] Task started: fastANI
[2024-01-24 12:09:47,973] [INFO] Running command: fastANI --query /var/lib/cwl/stga5122545-6a4e-451d-801d-0e72f55885b0/GCF_025137375.1_ASM2513737v1_genomic.fna.gz --refList GCF_025137375.1_ASM2513737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025137375.1_ASM2513737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:17,353] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:17,368] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:10:17,368] [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_014647515.1	s__Dactylosporangium sucinum	85.1016	2220	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716715.1	s__Dactylosporangium aurantiacum	82.5497	2031	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	82.4969	2035	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	78.5364	978	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011947195.1	s__Planosporangium thailandense	78.4279	1027	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	78.3442	1080	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	78.3158	1049	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	78.2788	1020	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091565.1	s__Micromonospora marina	78.2415	964	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.96	0.90	0.86	3	-
GCF_003725545.1	s__Micromonospora sp003725545	78.222	934	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_018324255.1	s__Polymorphospora rubra	78.0332	1181	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	77.8535	1058	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_018397995.1	s__NBRC-107566 sp018397995	77.8415	953	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__NBRC-107566	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090265.1	s__Micromonospora rifamycinica	77.8179	1048	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863615.1	s__Virgisporangium aliadipatigenens	77.712	1233	3498	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:17,370] [INFO] GTDB search result was written to GCF_025137375.1_ASM2513737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:17,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:17,375] [INFO] DFAST_QC result json was written to GCF_025137375.1_ASM2513737v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:17,375] [INFO] DFAST_QC completed!
[2024-01-24 12:10:17,375] [INFO] Total running time: 0h4m51s