[2024-01-24 12:14:35,192] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,194] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e1ff2f9-42c1-4ba8-95ce-2af45894c188/dqc_reference
[2024-01-24 12:14:36,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,521] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,521] [INFO] Running command: gunzip -c /var/lib/cwl/stg02f461b8-8796-402d-93bf-97af1608bd7d/GCF_019904175.1_ASM1990417v1_genomic.fna.gz | prodigal -d GCF_019904175.1_ASM1990417v1_genomic.fna/cds.fna -a GCF_019904175.1_ASM1990417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:20,916] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:20,916] [INFO] Task started: HMMsearch
[2024-01-24 12:15:20,916] [INFO] Running command: hmmsearch --tblout GCF_019904175.1_ASM1990417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e1ff2f9-42c1-4ba8-95ce-2af45894c188/dqc_reference/reference_markers.hmm GCF_019904175.1_ASM1990417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:21,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:21,374] [INFO] Found 6/6 markers.
[2024-01-24 12:15:21,459] [INFO] Query marker FASTA was written to GCF_019904175.1_ASM1990417v1_genomic.fna/markers.fasta
[2024-01-24 12:15:21,459] [INFO] Task started: Blastn
[2024-01-24 12:15:21,459] [INFO] Running command: blastn -query GCF_019904175.1_ASM1990417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e1ff2f9-42c1-4ba8-95ce-2af45894c188/dqc_reference/reference_markers.fasta -out GCF_019904175.1_ASM1990417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:22,682] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:22,685] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:22,685] [INFO] Target genome list was writen to GCF_019904175.1_ASM1990417v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:22,690] [INFO] Task started: fastANI
[2024-01-24 12:15:22,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f461b8-8796-402d-93bf-97af1608bd7d/GCF_019904175.1_ASM1990417v1_genomic.fna.gz --refList GCF_019904175.1_ASM1990417v1_genomic.fna/target_genomes.txt --output GCF_019904175.1_ASM1990417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:52,402] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:52,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e1ff2f9-42c1-4ba8-95ce-2af45894c188/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:52,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e1ff2f9-42c1-4ba8-95ce-2af45894c188/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:52,416] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:52,416] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:15:52,416] [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 vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	100.0	3985	3986	95	inconclusive
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	97.7734	3328	3986	95	inconclusive
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	81.6766	2093	3986	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	81.622	1892	3986	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	81.3029	2196	3986	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	81.2736	1606	3986	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	81.1964	2198	3986	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	80.9383	2138	3986	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	77.6812	1003	3986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:52,418] [INFO] DFAST Taxonomy check result was written to GCF_019904175.1_ASM1990417v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:52,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:52,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:52,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e1ff2f9-42c1-4ba8-95ce-2af45894c188/dqc_reference/checkm_data
[2024-01-24 12:15:52,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:52,525] [INFO] Task started: CheckM
[2024-01-24 12:15:52,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019904175.1_ASM1990417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019904175.1_ASM1990417v1_genomic.fna/checkm_input GCF_019904175.1_ASM1990417v1_genomic.fna/checkm_result
[2024-01-24 12:19:16,601] [INFO] Task succeeded: CheckM
[2024-01-24 12:19:16,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:19:16,626] [INFO] ===== Completeness check finished =====
[2024-01-24 12:19:16,626] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:19:16,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019904175.1_ASM1990417v1_genomic.fna/markers.fasta)
[2024-01-24 12:19:16,627] [INFO] Task started: Blastn
[2024-01-24 12:19:16,627] [INFO] Running command: blastn -query GCF_019904175.1_ASM1990417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e1ff2f9-42c1-4ba8-95ce-2af45894c188/dqc_reference/reference_markers_gtdb.fasta -out GCF_019904175.1_ASM1990417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:19:18,531] [INFO] Task succeeded: Blastn
[2024-01-24 12:19:18,534] [INFO] Selected 19 target genomes.
[2024-01-24 12:19:18,535] [INFO] Target genome list was writen to GCF_019904175.1_ASM1990417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:19:18,701] [INFO] Task started: fastANI
[2024-01-24 12:19:18,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f461b8-8796-402d-93bf-97af1608bd7d/GCF_019904175.1_ASM1990417v1_genomic.fna.gz --refList GCF_019904175.1_ASM1990417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019904175.1_ASM1990417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:20:00,094] [INFO] Task succeeded: fastANI
[2024-01-24 12:20:00,114] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:20:00,114] [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	81.669	2096	3986	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	81.2355	2184	3986	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	80.9339	2133	3986	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	78.0248	1059	3986	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	77.9705	1041	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830265.1	s__Micromonospora olivasterospora	77.8093	1058	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070575.1	s__Micromonospora sp018070575	77.7659	1095	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	77.7366	1242	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018397995.1	s__NBRC-107566 sp018397995	77.659	1017	3986	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_016862275.1	s__Actinoplanes nipponensis	77.6047	1409	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863615.1	s__Virgisporangium aliadipatigenens	77.5832	1430	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083965.1	s__Catellatospora sp019083965	77.5407	1248	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018327705.1	s__Catellatospora sp018327705	77.4864	1375	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	77.4498	1289	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_016862575.1	s__Catellatospora bangladeshensis	77.4356	1353	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_900091615.1	s__Micromonospora yangpuensis	77.3928	1003	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001567585.1	s__Micromonospora rosaria	77.3535	1082	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	77.3118	1310	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000717135.1	s__Catenuloplanes japonicus	77.0824	1427	3986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catenuloplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:20:00,116] [INFO] GTDB search result was written to GCF_019904175.1_ASM1990417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:20:00,116] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:20:00,121] [INFO] DFAST_QC result json was written to GCF_019904175.1_ASM1990417v1_genomic.fna/dqc_result.json
[2024-01-24 12:20:00,121] [INFO] DFAST_QC completed!
[2024-01-24 12:20:00,122] [INFO] Total running time: 0h5m25s