[2024-01-24 12:15:03,688] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,693] [INFO] DQC Reference Directory: /var/lib/cwl/stgcecc6fa4-003b-426b-94ae-bf1fd924e8dd/dqc_reference
[2024-01-24 12:15:04,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:04,919] [INFO] Task started: Prodigal
[2024-01-24 12:15:04,919] [INFO] Running command: gunzip -c /var/lib/cwl/stgef6d486e-c205-433c-aaa0-226f4a836868/GCF_016862155.1_ASM1686215v1_genomic.fna.gz | prodigal -d GCF_016862155.1_ASM1686215v1_genomic.fna/cds.fna -a GCF_016862155.1_ASM1686215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:32,101] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:32,102] [INFO] Task started: HMMsearch
[2024-01-24 12:15:32,102] [INFO] Running command: hmmsearch --tblout GCF_016862155.1_ASM1686215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcecc6fa4-003b-426b-94ae-bf1fd924e8dd/dqc_reference/reference_markers.hmm GCF_016862155.1_ASM1686215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:32,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:32,505] [INFO] Found 6/6 markers.
[2024-01-24 12:15:32,574] [INFO] Query marker FASTA was written to GCF_016862155.1_ASM1686215v1_genomic.fna/markers.fasta
[2024-01-24 12:15:32,575] [INFO] Task started: Blastn
[2024-01-24 12:15:32,575] [INFO] Running command: blastn -query GCF_016862155.1_ASM1686215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcecc6fa4-003b-426b-94ae-bf1fd924e8dd/dqc_reference/reference_markers.fasta -out GCF_016862155.1_ASM1686215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:33,782] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:33,785] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:33,785] [INFO] Target genome list was writen to GCF_016862155.1_ASM1686215v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:33,789] [INFO] Task started: fastANI
[2024-01-24 12:15:33,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgef6d486e-c205-433c-aaa0-226f4a836868/GCF_016862155.1_ASM1686215v1_genomic.fna.gz --refList GCF_016862155.1_ASM1686215v1_genomic.fna/target_genomes.txt --output GCF_016862155.1_ASM1686215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:00,185] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:00,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcecc6fa4-003b-426b-94ae-bf1fd924e8dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:00,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcecc6fa4-003b-426b-94ae-bf1fd924e8dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:00,199] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:16:00,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:00,199] [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 digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	100.0	2953	2960	95	conclusive
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	99.998	2959	2960	95	conclusive
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	85.1997	1832	2960	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	85.0925	1840	2960	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	84.9504	1832	2960	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	82.543	1553	2960	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.6314	1552	2960	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.3669	1026	2960	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.2373	1182	2960	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.8353	1006	2960	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.8223	1180	2960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:00,201] [INFO] DFAST Taxonomy check result was written to GCF_016862155.1_ASM1686215v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:00,202] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:00,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:00,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcecc6fa4-003b-426b-94ae-bf1fd924e8dd/dqc_reference/checkm_data
[2024-01-24 12:16:00,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:00,289] [INFO] Task started: CheckM
[2024-01-24 12:16:00,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862155.1_ASM1686215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862155.1_ASM1686215v1_genomic.fna/checkm_input GCF_016862155.1_ASM1686215v1_genomic.fna/checkm_result
[2024-01-24 12:17:15,895] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:15,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:15,925] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:15,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:15,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862155.1_ASM1686215v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:15,926] [INFO] Task started: Blastn
[2024-01-24 12:17:15,926] [INFO] Running command: blastn -query GCF_016862155.1_ASM1686215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcecc6fa4-003b-426b-94ae-bf1fd924e8dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862155.1_ASM1686215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:17,778] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:17,782] [INFO] Selected 10 target genomes.
[2024-01-24 12:17:17,782] [INFO] Target genome list was writen to GCF_016862155.1_ASM1686215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:17,791] [INFO] Task started: fastANI
[2024-01-24 12:17:17,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgef6d486e-c205-433c-aaa0-226f4a836868/GCF_016862155.1_ASM1686215v1_genomic.fna.gz --refList GCF_016862155.1_ASM1686215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862155.1_ASM1686215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:41,440] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:41,455] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:41,456] [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_014205335.1	s__Actinoplanes digitatis	99.998	2959	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000494755.1	s__Actinoplanes friuliensis	85.1823	1835	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862275.1	s__Actinoplanes nipponensis	85.0768	1844	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332655.1	s__Actinoplanes auranticolor	84.9355	1835	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	83.0844	1663	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_014648355.1	s__Actinoplanes azureus	82.8316	1529	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464385.1	s__Actinoplanes sp016464385	82.8172	1691	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	81.6922	1383	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	81.6777	1548	2960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553785.1	s__Actinoplanes sp001553785	81.3465	1355	2960	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 12:17:41,457] [INFO] GTDB search result was written to GCF_016862155.1_ASM1686215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:41,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:41,461] [INFO] DFAST_QC result json was written to GCF_016862155.1_ASM1686215v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:41,461] [INFO] DFAST_QC completed!
[2024-01-24 12:17:41,461] [INFO] Total running time: 0h2m38s