[2024-01-25 17:42:35,442] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:35,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:35,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a2a1a18-565c-45ef-8c17-5288d93da8d3/dqc_reference
[2024-01-25 17:42:36,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:36,560] [INFO] Task started: Prodigal
[2024-01-25 17:42:36,560] [INFO] Running command: gunzip -c /var/lib/cwl/stge7787977-1999-4b48-890d-300d1b4aeaef/GCF_016862795.1_ASM1686279v1_genomic.fna.gz | prodigal -d GCF_016862795.1_ASM1686279v1_genomic.fna/cds.fna -a GCF_016862795.1_ASM1686279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:11,242] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:11,242] [INFO] Task started: HMMsearch
[2024-01-25 17:43:11,242] [INFO] Running command: hmmsearch --tblout GCF_016862795.1_ASM1686279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a2a1a18-565c-45ef-8c17-5288d93da8d3/dqc_reference/reference_markers.hmm GCF_016862795.1_ASM1686279v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:11,752] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:11,753] [INFO] Found 6/6 markers.
[2024-01-25 17:43:11,867] [INFO] Query marker FASTA was written to GCF_016862795.1_ASM1686279v1_genomic.fna/markers.fasta
[2024-01-25 17:43:11,868] [INFO] Task started: Blastn
[2024-01-25 17:43:11,868] [INFO] Running command: blastn -query GCF_016862795.1_ASM1686279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a2a1a18-565c-45ef-8c17-5288d93da8d3/dqc_reference/reference_markers.fasta -out GCF_016862795.1_ASM1686279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:13,101] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:13,106] [INFO] Selected 9 target genomes.
[2024-01-25 17:43:13,106] [INFO] Target genome list was writen to GCF_016862795.1_ASM1686279v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:13,120] [INFO] Task started: fastANI
[2024-01-25 17:43:13,120] [INFO] Running command: fastANI --query /var/lib/cwl/stge7787977-1999-4b48-890d-300d1b4aeaef/GCF_016862795.1_ASM1686279v1_genomic.fna.gz --refList GCF_016862795.1_ASM1686279v1_genomic.fna/target_genomes.txt --output GCF_016862795.1_ASM1686279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:44,171] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:44,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a2a1a18-565c-45ef-8c17-5288d93da8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:44,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a2a1a18-565c-45ef-8c17-5288d93da8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:44,179] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:44,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:44,179] [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 siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	100.0	4087	4100	95	conclusive
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	88.1341	2738	4100	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	88.1097	2716	4100	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	82.3902	2089	4100	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	82.2217	2255	4100	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	81.8451	1664	4100	95	below_threshold
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	80.9672	2149	4100	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	80.8968	2096	4100	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.0089	1065	4100	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:44,180] [INFO] DFAST Taxonomy check result was written to GCF_016862795.1_ASM1686279v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:44,181] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:44,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:44,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a2a1a18-565c-45ef-8c17-5288d93da8d3/dqc_reference/checkm_data
[2024-01-25 17:43:44,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:44,293] [INFO] Task started: CheckM
[2024-01-25 17:43:44,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862795.1_ASM1686279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862795.1_ASM1686279v1_genomic.fna/checkm_input GCF_016862795.1_ASM1686279v1_genomic.fna/checkm_result
[2024-01-25 17:47:07,814] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:07,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:07,847] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:07,847] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:07,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862795.1_ASM1686279v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:07,848] [INFO] Task started: Blastn
[2024-01-25 17:47:07,848] [INFO] Running command: blastn -query GCF_016862795.1_ASM1686279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a2a1a18-565c-45ef-8c17-5288d93da8d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862795.1_ASM1686279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:09,856] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:09,860] [INFO] Selected 19 target genomes.
[2024-01-25 17:47:09,860] [INFO] Target genome list was writen to GCF_016862795.1_ASM1686279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:09,879] [INFO] Task started: fastANI
[2024-01-25 17:47:09,879] [INFO] Running command: fastANI --query /var/lib/cwl/stge7787977-1999-4b48-890d-300d1b4aeaef/GCF_016862795.1_ASM1686279v1_genomic.fna.gz --refList GCF_016862795.1_ASM1686279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862795.1_ASM1686279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:56,192] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:56,205] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:56,205] [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_016862795.1	s__Dactylosporangium siamense	100.0	4087	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000716715.1	s__Dactylosporangium aurantiacum	88.1013	2718	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647515.1	s__Dactylosporangium sucinum	82.2405	2251	4100	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	78.087	1062	4100	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	77.9951	1086	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011297335.1	s__Catellatospora methionotrophica	77.9518	1356	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	77.8931	1227	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_900090305.1	s__Micromonospora siamensis	77.8793	1149	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	77.857	1340	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_003434305.1	s__Micromonospora sp003434305	77.8456	1225	4100	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	77.7935	1223	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	77.78	1340	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_018327705.1	s__Catellatospora sp018327705	77.7535	1490	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000982955.1	s__Micromonospora sp000982955	77.7091	1194	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188485.1	s__Asanoa hainanensis	77.6807	1304	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091545.1	s__Micromonospora viridifaciens	77.6395	1127	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	77.3057	1282	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_000717135.1	s__Catenuloplanes japonicus	77.2361	1472	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catenuloplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	77.2054	1306	4100	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:56,207] [INFO] GTDB search result was written to GCF_016862795.1_ASM1686279v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:56,207] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:56,210] [INFO] DFAST_QC result json was written to GCF_016862795.1_ASM1686279v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:56,210] [INFO] DFAST_QC completed!
[2024-01-25 17:47:56,210] [INFO] Total running time: 0h5m21s