[2024-01-24 11:59:35,290] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,292] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,293] [INFO] DQC Reference Directory: /var/lib/cwl/stg25a6e947-5a0c-4382-88f7-861f3fad8ffb/dqc_reference
[2024-01-24 11:59:36,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,513] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,513] [INFO] Running command: gunzip -c /var/lib/cwl/stge439dcca-2ae2-4423-958d-78fc27711deb/GCF_016862175.1_ASM1686217v1_genomic.fna.gz | prodigal -d GCF_016862175.1_ASM1686217v1_genomic.fna/cds.fna -a GCF_016862175.1_ASM1686217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:07,446] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:07,446] [INFO] Task started: HMMsearch
[2024-01-24 12:00:07,446] [INFO] Running command: hmmsearch --tblout GCF_016862175.1_ASM1686217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25a6e947-5a0c-4382-88f7-861f3fad8ffb/dqc_reference/reference_markers.hmm GCF_016862175.1_ASM1686217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:07,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:07,955] [INFO] Found 6/6 markers.
[2024-01-24 12:00:08,038] [INFO] Query marker FASTA was written to GCF_016862175.1_ASM1686217v1_genomic.fna/markers.fasta
[2024-01-24 12:00:08,039] [INFO] Task started: Blastn
[2024-01-24 12:00:08,039] [INFO] Running command: blastn -query GCF_016862175.1_ASM1686217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a6e947-5a0c-4382-88f7-861f3fad8ffb/dqc_reference/reference_markers.fasta -out GCF_016862175.1_ASM1686217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:09,410] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:09,413] [INFO] Selected 22 target genomes.
[2024-01-24 12:00:09,414] [INFO] Target genome list was writen to GCF_016862175.1_ASM1686217v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:09,434] [INFO] Task started: fastANI
[2024-01-24 12:00:09,435] [INFO] Running command: fastANI --query /var/lib/cwl/stge439dcca-2ae2-4423-958d-78fc27711deb/GCF_016862175.1_ASM1686217v1_genomic.fna.gz --refList GCF_016862175.1_ASM1686217v1_genomic.fna/target_genomes.txt --output GCF_016862175.1_ASM1686217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:01,159] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:01,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25a6e947-5a0c-4382-88f7-861f3fad8ffb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:01,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25a6e947-5a0c-4382-88f7-861f3fad8ffb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:01,183] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:01:01,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:01:01,184] [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
Actinoplanes durhamensis	strain=NBRC 14914	GCA_016862175.1	113563	113563	type	True	100.0	3428	3432	95	conclusive
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	87.6051	2582	3432	95	below_threshold
Actinoplanes toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	87.6009	2429	3432	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	85.6664	2089	3432	95	below_threshold
Actinoplanes globisporus	strain=DSM 43857	GCA_000379645.1	113565	113565	type	True	84.0427	2138	3432	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	83.7895	2060	3432	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	83.0845	1972	3432	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	82.3548	1939	3432	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	82.2043	1904	3432	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	82.0951	1805	3432	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	82.0379	1931	3432	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	81.9524	1985	3432	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.8501	1671	3432	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.9808	845	3432	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.843	1203	3432	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.7514	1028	3432	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	77.9	1175	3432	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	77.8619	1176	3432	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	77.8227	1169	3432	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	77.7998	1211	3432	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.5493	1343	3432	95	below_threshold
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	77.0746	762	3432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:01,185] [INFO] DFAST Taxonomy check result was written to GCF_016862175.1_ASM1686217v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:01,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:01,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:01,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25a6e947-5a0c-4382-88f7-861f3fad8ffb/dqc_reference/checkm_data
[2024-01-24 12:01:01,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:01,282] [INFO] Task started: CheckM
[2024-01-24 12:01:01,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862175.1_ASM1686217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862175.1_ASM1686217v1_genomic.fna/checkm_input GCF_016862175.1_ASM1686217v1_genomic.fna/checkm_result
[2024-01-24 12:02:40,373] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:40,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:02:40,403] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:40,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:40,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862175.1_ASM1686217v1_genomic.fna/markers.fasta)
[2024-01-24 12:02:40,404] [INFO] Task started: Blastn
[2024-01-24 12:02:40,404] [INFO] Running command: blastn -query GCF_016862175.1_ASM1686217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a6e947-5a0c-4382-88f7-861f3fad8ffb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862175.1_ASM1686217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:02:42,444] [INFO] Task succeeded: Blastn
[2024-01-24 12:02:42,448] [INFO] Selected 13 target genomes.
[2024-01-24 12:02:42,449] [INFO] Target genome list was writen to GCF_016862175.1_ASM1686217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:02:42,458] [INFO] Task started: fastANI
[2024-01-24 12:02:42,459] [INFO] Running command: fastANI --query /var/lib/cwl/stge439dcca-2ae2-4423-958d-78fc27711deb/GCF_016862175.1_ASM1686217v1_genomic.fna.gz --refList GCF_016862175.1_ASM1686217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862175.1_ASM1686217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:03:19,171] [INFO] Task succeeded: fastANI
[2024-01-24 12:03:19,187] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:03:19,187] [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_016862175.1	s__Actinoplanes durhamensis	100.0	3428	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862435.1	s__Actinoplanes tereljensis	87.6245	2579	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332695.1	s__Actinoplanes toevensis	87.6183	2427	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862195.1	s__Actinoplanes ferrugineus	85.6569	2090	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379645.1	s__Actinoplanes globisporus	84.0607	2133	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721705.1	s__Actinoplanes subtropicus	83.7495	2069	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862375.1	s__Actinoplanes rishiriensis	83.074	1973	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	82.2946	1954	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	82.203	1905	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	82.1152	1801	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018829635.1	s__Actinoplanes bogorensis	82.0466	1928	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016834655.1	s__Actinoplanes sp016834655	81.9375	1986	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	81.7738	1770	3432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:03:19,188] [INFO] GTDB search result was written to GCF_016862175.1_ASM1686217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:03:19,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:03:19,193] [INFO] DFAST_QC result json was written to GCF_016862175.1_ASM1686217v1_genomic.fna/dqc_result.json
[2024-01-24 12:03:19,193] [INFO] DFAST_QC completed!
[2024-01-24 12:03:19,194] [INFO] Total running time: 0h3m44s