[2024-01-24 13:22:12,382] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:12,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:12,383] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1e595cc-8db7-43c8-8be1-9655929bd31c/dqc_reference
[2024-01-24 13:22:13,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,668] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg29203b18-a388-44ce-8851-9c5641323851/GCF_003389455.1_ASM338945v1_genomic.fna.gz | prodigal -d GCF_003389455.1_ASM338945v1_genomic.fna/cds.fna -a GCF_003389455.1_ASM338945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:39,307] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:39,307] [INFO] Task started: HMMsearch
[2024-01-24 13:22:39,308] [INFO] Running command: hmmsearch --tblout GCF_003389455.1_ASM338945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1e595cc-8db7-43c8-8be1-9655929bd31c/dqc_reference/reference_markers.hmm GCF_003389455.1_ASM338945v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:39,911] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:39,912] [INFO] Found 6/6 markers.
[2024-01-24 13:22:40,009] [INFO] Query marker FASTA was written to GCF_003389455.1_ASM338945v1_genomic.fna/markers.fasta
[2024-01-24 13:22:40,010] [INFO] Task started: Blastn
[2024-01-24 13:22:40,010] [INFO] Running command: blastn -query GCF_003389455.1_ASM338945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1e595cc-8db7-43c8-8be1-9655929bd31c/dqc_reference/reference_markers.fasta -out GCF_003389455.1_ASM338945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:41,549] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:41,553] [INFO] Selected 17 target genomes.
[2024-01-24 13:22:41,553] [INFO] Target genome list was writen to GCF_003389455.1_ASM338945v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:41,559] [INFO] Task started: fastANI
[2024-01-24 13:22:41,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg29203b18-a388-44ce-8851-9c5641323851/GCF_003389455.1_ASM338945v1_genomic.fna.gz --refList GCF_003389455.1_ASM338945v1_genomic.fna/target_genomes.txt --output GCF_003389455.1_ASM338945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:17,846] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:17,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1e595cc-8db7-43c8-8be1-9655929bd31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:17,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1e595cc-8db7-43c8-8be1-9655929bd31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:17,864] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:17,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:17,865] [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
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	100.0	2904	2927	95	conclusive
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	89.6003	1951	2927	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	89.5901	2076	2927	95	below_threshold
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	89.5879	2078	2927	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	89.5715	2030	2927	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	89.3491	1983	2927	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	89.1665	1913	2927	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	89.1214	1966	2927	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	89.0966	2039	2927	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	88.84	1764	2927	95	below_threshold
Streptomyces lydicus	strain=ATCC 25470	GCA_004125245.1	47763	47763	suspected-type	True	88.6635	1961	2927	95	below_threshold
Streptomyces lydicus	strain=NRRL ISP-5461	GCA_000717345.1	47763	47763	suspected-type	True	88.5827	1977	2927	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.7275	1581	2927	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.4555	1229	2927	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.7671	1607	2927	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.6701	1563	2927	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.6189	1633	2927	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:17,866] [INFO] DFAST Taxonomy check result was written to GCF_003389455.1_ASM338945v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:17,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:17,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:17,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1e595cc-8db7-43c8-8be1-9655929bd31c/dqc_reference/checkm_data
[2024-01-24 13:23:17,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:17,952] [INFO] Task started: CheckM
[2024-01-24 13:23:17,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003389455.1_ASM338945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003389455.1_ASM338945v1_genomic.fna/checkm_input GCF_003389455.1_ASM338945v1_genomic.fna/checkm_result
[2024-01-24 13:24:39,818] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:39,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 13:24:39,843] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:39,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:39,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003389455.1_ASM338945v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:39,844] [INFO] Task started: Blastn
[2024-01-24 13:24:39,844] [INFO] Running command: blastn -query GCF_003389455.1_ASM338945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1e595cc-8db7-43c8-8be1-9655929bd31c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003389455.1_ASM338945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:42,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:42,180] [INFO] Selected 12 target genomes.
[2024-01-24 13:24:42,180] [INFO] Target genome list was writen to GCF_003389455.1_ASM338945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:42,239] [INFO] Task started: fastANI
[2024-01-24 13:24:42,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg29203b18-a388-44ce-8851-9c5641323851/GCF_003389455.1_ASM338945v1_genomic.fna.gz --refList GCF_003389455.1_ASM338945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003389455.1_ASM338945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:08,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:08,177] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:08,177] [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_003389455.1	s__Streptomyces inhibens	100.0	2904	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001270575.1	s__Streptomyces decoyicus	89.5923	1952	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811595.1	s__Streptomyces libani	89.5707	2081	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_009811555.1	s__Streptomyces caniferus	89.107	2037	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704855.1	s__Streptomyces platensis	89.0868	1971	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_009811635.1	s__Streptomyces tubercidicus	88.9705	1836	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	88.8794	1866	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_900187385.1	s__Streptomyces sp900187385	88.8676	1873	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_004122735.1	s__Streptomyces sioyaensis	88.8369	1766	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_004125265.1	s__Streptomyces lydicus_C	88.7712	1875	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717345.1	s__Streptomyces lydicus	88.5874	1977	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.38	0.95	0.89	6	-
GCF_014646275.1	s__Streptomyces kronopolitis	88.2689	1765	2927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:08,179] [INFO] GTDB search result was written to GCF_003389455.1_ASM338945v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:08,180] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:08,183] [INFO] DFAST_QC result json was written to GCF_003389455.1_ASM338945v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:08,183] [INFO] DFAST_QC completed!
[2024-01-24 13:25:08,184] [INFO] Total running time: 0h2m56s