[2024-01-24 12:15:19,495] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:19,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:19,497] [INFO] DQC Reference Directory: /var/lib/cwl/stge92dadd0-cbf6-4067-b03f-3cd43525083a/dqc_reference
[2024-01-24 12:15:20,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,820] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg660f7f38-6cd0-468b-851f-ed902fe3da89/GCF_015645455.1_ASM1564545v1_genomic.fna.gz | prodigal -d GCF_015645455.1_ASM1564545v1_genomic.fna/cds.fna -a GCF_015645455.1_ASM1564545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:44,902] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:44,903] [INFO] Task started: HMMsearch
[2024-01-24 12:15:44,903] [INFO] Running command: hmmsearch --tblout GCF_015645455.1_ASM1564545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge92dadd0-cbf6-4067-b03f-3cd43525083a/dqc_reference/reference_markers.hmm GCF_015645455.1_ASM1564545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:45,280] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:45,281] [INFO] Found 6/6 markers.
[2024-01-24 12:15:45,350] [INFO] Query marker FASTA was written to GCF_015645455.1_ASM1564545v1_genomic.fna/markers.fasta
[2024-01-24 12:15:45,350] [INFO] Task started: Blastn
[2024-01-24 12:15:45,350] [INFO] Running command: blastn -query GCF_015645455.1_ASM1564545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge92dadd0-cbf6-4067-b03f-3cd43525083a/dqc_reference/reference_markers.fasta -out GCF_015645455.1_ASM1564545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:46,677] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:46,680] [INFO] Selected 15 target genomes.
[2024-01-24 12:15:46,681] [INFO] Target genome list was writen to GCF_015645455.1_ASM1564545v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:46,686] [INFO] Task started: fastANI
[2024-01-24 12:15:46,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg660f7f38-6cd0-468b-851f-ed902fe3da89/GCF_015645455.1_ASM1564545v1_genomic.fna.gz --refList GCF_015645455.1_ASM1564545v1_genomic.fna/target_genomes.txt --output GCF_015645455.1_ASM1564545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:18,890] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:18,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge92dadd0-cbf6-4067-b03f-3cd43525083a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:18,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge92dadd0-cbf6-4067-b03f-3cd43525083a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:18,909] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:16:18,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:18,909] [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_015645455.1	47716	47716	type	True	100.0	2677	2682	95	conclusive
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	98.1004	2436	2682	95	conclusive
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	90.2011	1982	2682	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	90.0879	1991	2682	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	90.0489	1941	2682	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	90.0474	1991	2682	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	89.9114	1853	2682	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	89.8109	1950	2682	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	88.3712	1775	2682	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	88.3216	1765	2682	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.3049	1779	2682	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.6491	1465	2682	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	84.9148	1703	2682	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	84.7306	1398	2682	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.1342	1527	2682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:18,911] [INFO] DFAST Taxonomy check result was written to GCF_015645455.1_ASM1564545v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:18,912] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:18,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:18,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge92dadd0-cbf6-4067-b03f-3cd43525083a/dqc_reference/checkm_data
[2024-01-24 12:16:18,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:18,987] [INFO] Task started: CheckM
[2024-01-24 12:16:18,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015645455.1_ASM1564545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015645455.1_ASM1564545v1_genomic.fna/checkm_input GCF_015645455.1_ASM1564545v1_genomic.fna/checkm_result
[2024-01-24 12:18:11,444] [INFO] Task succeeded: CheckM
[2024-01-24 12:18:11,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:18:11,481] [INFO] ===== Completeness check finished =====
[2024-01-24 12:18:11,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:18:11,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015645455.1_ASM1564545v1_genomic.fna/markers.fasta)
[2024-01-24 12:18:11,482] [INFO] Task started: Blastn
[2024-01-24 12:18:11,482] [INFO] Running command: blastn -query GCF_015645455.1_ASM1564545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge92dadd0-cbf6-4067-b03f-3cd43525083a/dqc_reference/reference_markers_gtdb.fasta -out GCF_015645455.1_ASM1564545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:18:13,598] [INFO] Task succeeded: Blastn
[2024-01-24 12:18:13,604] [INFO] Selected 16 target genomes.
[2024-01-24 12:18:13,604] [INFO] Target genome list was writen to GCF_015645455.1_ASM1564545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:18:13,614] [INFO] Task started: fastANI
[2024-01-24 12:18:13,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg660f7f38-6cd0-468b-851f-ed902fe3da89/GCF_015645455.1_ASM1564545v1_genomic.fna.gz --refList GCF_015645455.1_ASM1564545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015645455.1_ASM1564545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:48,069] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:48,089] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:48,089] [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	98.1004	2436	2682	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	93.1016	2094	2682	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	90.4657	1857	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_014650435.1	s__Streptomyces tendae	90.1932	1983	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_003369795.1	s__Streptomyces sp003369795	90.1598	1860	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3499	N/A	N/A	N/A	N/A	1	-
GCF_003112595.1	s__Streptomyces rubrogriseus	90.0761	1993	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	90.0594	1969	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_014651155.1	s__Streptomyces anthocyanicus	90.027	1994	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	-
GCF_000717995.1	s__Streptomyces violaceorubidus	89.9232	1853	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772045.1	s__Streptomyces sp000772045	89.9092	1977	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_019049325.1	s__Streptomyces sp019049325	89.8887	1995	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112575.1	s__Streptomyces ardesiacus	89.8483	1945	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_004364245.1	s__Streptomyces sp004364245	89.6833	1866	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671715.1	s__Streptomyces sp003671715	89.2242	1845	2682	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	89.0538	1845	2682	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	88.3495	1777	2682	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 12:18:48,091] [INFO] GTDB search result was written to GCF_015645455.1_ASM1564545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:48,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:48,096] [INFO] DFAST_QC result json was written to GCF_015645455.1_ASM1564545v1_genomic.fna/dqc_result.json
[2024-01-24 12:18:48,097] [INFO] DFAST_QC completed!
[2024-01-24 12:18:48,097] [INFO] Total running time: 0h3m29s