[2024-01-25 18:53:50,824] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:50,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:50,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg771f14b4-4933-45b0-9781-850cd22e62f5/dqc_reference
[2024-01-25 18:53:52,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:52,039] [INFO] Task started: Prodigal
[2024-01-25 18:53:52,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg9028c6e6-774b-4e62-b769-b02ca1bcc42c/GCF_025264685.1_ASM2526468v1_genomic.fna.gz | prodigal -d GCF_025264685.1_ASM2526468v1_genomic.fna/cds.fna -a GCF_025264685.1_ASM2526468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:15,362] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:15,362] [INFO] Task started: HMMsearch
[2024-01-25 18:54:15,362] [INFO] Running command: hmmsearch --tblout GCF_025264685.1_ASM2526468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg771f14b4-4933-45b0-9781-850cd22e62f5/dqc_reference/reference_markers.hmm GCF_025264685.1_ASM2526468v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:15,663] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:15,665] [INFO] Found 6/6 markers.
[2024-01-25 18:54:15,728] [INFO] Query marker FASTA was written to GCF_025264685.1_ASM2526468v1_genomic.fna/markers.fasta
[2024-01-25 18:54:15,728] [INFO] Task started: Blastn
[2024-01-25 18:54:15,728] [INFO] Running command: blastn -query GCF_025264685.1_ASM2526468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg771f14b4-4933-45b0-9781-850cd22e62f5/dqc_reference/reference_markers.fasta -out GCF_025264685.1_ASM2526468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:16,865] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:16,868] [INFO] Selected 10 target genomes.
[2024-01-25 18:54:16,868] [INFO] Target genome list was writen to GCF_025264685.1_ASM2526468v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:16,872] [INFO] Task started: fastANI
[2024-01-25 18:54:16,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg9028c6e6-774b-4e62-b769-b02ca1bcc42c/GCF_025264685.1_ASM2526468v1_genomic.fna.gz --refList GCF_025264685.1_ASM2526468v1_genomic.fna/target_genomes.txt --output GCF_025264685.1_ASM2526468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:41,914] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:41,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg771f14b4-4933-45b0-9781-850cd22e62f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:41,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg771f14b4-4933-45b0-9781-850cd22e62f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:41,922] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:54:41,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:41,922] [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 roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	100.0	2737	2740	95	conclusive
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	92.8057	1929	2740	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	84.4847	1761	2740	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	82.3444	1659	2740	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	82.3221	1638	2740	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	81.9919	1621	2740	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	81.4394	1539	2740	95	below_threshold
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	81.4095	1594	2740	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.3505	803	2740	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	77.8013	920	2740	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:41,924] [INFO] DFAST Taxonomy check result was written to GCF_025264685.1_ASM2526468v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:41,924] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:41,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:41,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg771f14b4-4933-45b0-9781-850cd22e62f5/dqc_reference/checkm_data
[2024-01-25 18:54:41,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:42,000] [INFO] Task started: CheckM
[2024-01-25 18:54:42,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025264685.1_ASM2526468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025264685.1_ASM2526468v1_genomic.fna/checkm_input GCF_025264685.1_ASM2526468v1_genomic.fna/checkm_result
[2024-01-25 18:56:42,683] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:42,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:42,702] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:42,702] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:42,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025264685.1_ASM2526468v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:42,704] [INFO] Task started: Blastn
[2024-01-25 18:56:42,704] [INFO] Running command: blastn -query GCF_025264685.1_ASM2526468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg771f14b4-4933-45b0-9781-850cd22e62f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_025264685.1_ASM2526468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:44,524] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:44,526] [INFO] Selected 16 target genomes.
[2024-01-25 18:56:44,527] [INFO] Target genome list was writen to GCF_025264685.1_ASM2526468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:44,543] [INFO] Task started: fastANI
[2024-01-25 18:56:44,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg9028c6e6-774b-4e62-b769-b02ca1bcc42c/GCF_025264685.1_ASM2526468v1_genomic.fna.gz --refList GCF_025264685.1_ASM2526468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025264685.1_ASM2526468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:13,363] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:13,373] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:57:13,373] [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	84.5182	1756	2740	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	82.2975	1643	2740	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	82.0235	1615	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011947195.1	s__Planosporangium thailandense	78.6694	896	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	78.637	884	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004217615.1	s__Micromonospora kangleipakensis	78.5215	945	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	78.5071	784	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091545.1	s__Micromonospora viridifaciens	78.4907	892	2740	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	78.3335	975	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091605.1	s__Micromonospora tulbaghiae	78.218	914	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_018397995.1	s__NBRC-107566 sp018397995	78.0029	875	2740	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_018324255.1	s__Polymorphospora rubra	77.9387	998	2740	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	77.8848	910	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCA_005885555.1	s__Rugosimonospora sp005885555	77.7674	835	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	77.7318	882	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861975.1	s__Actinocatenispora rupis	76.7916	835	2740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:13,374] [INFO] GTDB search result was written to GCF_025264685.1_ASM2526468v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:13,375] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:13,377] [INFO] DFAST_QC result json was written to GCF_025264685.1_ASM2526468v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:13,377] [INFO] DFAST_QC completed!
[2024-01-25 18:57:13,378] [INFO] Total running time: 0h3m23s