[2024-01-24 13:09:43,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:43,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:43,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg311a40e6-15d7-4607-a8af-abeae5af4085/dqc_reference
[2024-01-24 13:09:44,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:44,633] [INFO] Task started: Prodigal
[2024-01-24 13:09:44,634] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf5a4bf0-1373-4407-851b-654c87280457/GCF_000721235.1_ASM72123v1_genomic.fna.gz | prodigal -d GCF_000721235.1_ASM72123v1_genomic.fna/cds.fna -a GCF_000721235.1_ASM72123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:11,503] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:11,503] [INFO] Task started: HMMsearch
[2024-01-24 13:10:11,504] [INFO] Running command: hmmsearch --tblout GCF_000721235.1_ASM72123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg311a40e6-15d7-4607-a8af-abeae5af4085/dqc_reference/reference_markers.hmm GCF_000721235.1_ASM72123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:11,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:11,876] [INFO] Found 6/6 markers.
[2024-01-24 13:10:11,942] [INFO] Query marker FASTA was written to GCF_000721235.1_ASM72123v1_genomic.fna/markers.fasta
[2024-01-24 13:10:11,942] [INFO] Task started: Blastn
[2024-01-24 13:10:11,942] [INFO] Running command: blastn -query GCF_000721235.1_ASM72123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg311a40e6-15d7-4607-a8af-abeae5af4085/dqc_reference/reference_markers.fasta -out GCF_000721235.1_ASM72123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:13,272] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:13,276] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:13,277] [INFO] Target genome list was writen to GCF_000721235.1_ASM72123v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:13,290] [INFO] Task started: fastANI
[2024-01-24 13:10:13,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf5a4bf0-1373-4407-851b-654c87280457/GCF_000721235.1_ASM72123v1_genomic.fna.gz --refList GCF_000721235.1_ASM72123v1_genomic.fna/target_genomes.txt --output GCF_000721235.1_ASM72123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:49,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:49,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg311a40e6-15d7-4607-a8af-abeae5af4085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:49,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg311a40e6-15d7-4607-a8af-abeae5af4085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:49,158] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:49,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:49,159] [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 olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	100.0	2788	2794	95	conclusive
Streptomyces olivaceus	strain=NRRL B-3009	GCA_015645455.1	47716	47716	type	True	98.0741	2434	2794	95	conclusive
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	90.0492	2026	2794	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	89.9695	1987	2794	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	89.9569	2003	2794	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	89.9069	1940	2794	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	89.861	1838	2794	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	89.7463	1960	2794	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	88.484	1856	2794	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	88.3104	1776	2794	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	88.1861	1792	2794	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.2443	1776	2794	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.4317	1478	2794	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	84.7381	1726	2794	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	84.7212	1401	2794	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.0081	1546	2794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:49,161] [INFO] DFAST Taxonomy check result was written to GCF_000721235.1_ASM72123v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:49,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:49,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:49,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg311a40e6-15d7-4607-a8af-abeae5af4085/dqc_reference/checkm_data
[2024-01-24 13:10:49,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:49,244] [INFO] Task started: CheckM
[2024-01-24 13:10:49,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000721235.1_ASM72123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000721235.1_ASM72123v1_genomic.fna/checkm_input GCF_000721235.1_ASM72123v1_genomic.fna/checkm_result
[2024-01-24 13:12:50,922] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:50,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:50,950] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:50,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:50,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000721235.1_ASM72123v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:50,951] [INFO] Task started: Blastn
[2024-01-24 13:12:50,951] [INFO] Running command: blastn -query GCF_000721235.1_ASM72123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg311a40e6-15d7-4607-a8af-abeae5af4085/dqc_reference/reference_markers_gtdb.fasta -out GCF_000721235.1_ASM72123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:53,118] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:53,122] [INFO] Selected 15 target genomes.
[2024-01-24 13:12:53,122] [INFO] Target genome list was writen to GCF_000721235.1_ASM72123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:53,153] [INFO] Task started: fastANI
[2024-01-24 13:12:53,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf5a4bf0-1373-4407-851b-654c87280457/GCF_000721235.1_ASM72123v1_genomic.fna.gz --refList GCF_000721235.1_ASM72123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000721235.1_ASM72123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:26,654] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:26,722] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:26,722] [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_000721235.1	s__Streptomyces olivaceus	100.0	2788	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.53	98.10	0.91	0.89	6	conclusive
GCF_018982965.1	s__Streptomyces sp018982965	92.9953	2091	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939385.1	s__Streptomyces sp002939385	90.2499	1904	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_003369795.1	s__Streptomyces sp003369795	90.1309	1896	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3499	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	90.0371	2028	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_014651155.1	s__Streptomyces anthocyanicus	89.9627	1988	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	-
GCF_003112595.1	s__Streptomyces rubrogriseus	89.9533	2004	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_000772045.1	s__Streptomyces sp000772045	89.9317	1979	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_000717995.1	s__Streptomyces violaceorubidus	89.8691	1837	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	89.8607	2016	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_003112575.1	s__Streptomyces ardesiacus	89.7532	1961	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_003671715.1	s__Streptomyces sp003671715	89.2049	1843	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_001905385.1	s__Streptomyces sp001905385	88.8845	1876	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCF_014648815.1	s__Streptomyces flaveolus	88.2774	1780	2794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	88.1463	1695	2794	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 13:13:26,724] [INFO] GTDB search result was written to GCF_000721235.1_ASM72123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:26,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:26,729] [INFO] DFAST_QC result json was written to GCF_000721235.1_ASM72123v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:26,729] [INFO] DFAST_QC completed!
[2024-01-24 13:13:26,729] [INFO] Total running time: 0h3m43s