[2024-01-24 12:36:23,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,000] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,000] [INFO] DQC Reference Directory: /var/lib/cwl/stg237887c5-6888-4edf-967b-828d1c63ae43/dqc_reference
[2024-01-24 12:36:25,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,376] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg1228ecf2-18ab-4399-bbc1-732a189fecc1/GCF_014280945.1_ASM1428094v1_genomic.fna.gz | prodigal -d GCF_014280945.1_ASM1428094v1_genomic.fna/cds.fna -a GCF_014280945.1_ASM1428094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:48,579] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:48,579] [INFO] Task started: HMMsearch
[2024-01-24 12:36:48,579] [INFO] Running command: hmmsearch --tblout GCF_014280945.1_ASM1428094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg237887c5-6888-4edf-967b-828d1c63ae43/dqc_reference/reference_markers.hmm GCF_014280945.1_ASM1428094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:48,943] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:48,944] [INFO] Found 6/6 markers.
[2024-01-24 12:36:49,009] [INFO] Query marker FASTA was written to GCF_014280945.1_ASM1428094v1_genomic.fna/markers.fasta
[2024-01-24 12:36:49,009] [INFO] Task started: Blastn
[2024-01-24 12:36:49,009] [INFO] Running command: blastn -query GCF_014280945.1_ASM1428094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237887c5-6888-4edf-967b-828d1c63ae43/dqc_reference/reference_markers.fasta -out GCF_014280945.1_ASM1428094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:50,367] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:50,370] [INFO] Selected 11 target genomes.
[2024-01-24 12:36:50,370] [INFO] Target genome list was writen to GCF_014280945.1_ASM1428094v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:50,376] [INFO] Task started: fastANI
[2024-01-24 12:36:50,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg1228ecf2-18ab-4399-bbc1-732a189fecc1/GCF_014280945.1_ASM1428094v1_genomic.fna.gz --refList GCF_014280945.1_ASM1428094v1_genomic.fna/target_genomes.txt --output GCF_014280945.1_ASM1428094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:13,885] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:13,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg237887c5-6888-4edf-967b-828d1c63ae43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:13,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg237887c5-6888-4edf-967b-828d1c63ae43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:13,905] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:13,905] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:13,906] [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 tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	92.8167	2123	2773	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	92.8004	2061	2773	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	92.7478	2128	2773	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	92.6677	2141	2773	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	92.5233	2051	2773	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	92.389	1956	2773	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.8995	1898	2773	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.1677	1490	2773	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.2569	1482	2773	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.0331	1517	2773	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.6691	1559	2773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:13,908] [INFO] DFAST Taxonomy check result was written to GCF_014280945.1_ASM1428094v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:13,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:13,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:13,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg237887c5-6888-4edf-967b-828d1c63ae43/dqc_reference/checkm_data
[2024-01-24 12:37:13,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:13,988] [INFO] Task started: CheckM
[2024-01-24 12:37:13,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014280945.1_ASM1428094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014280945.1_ASM1428094v1_genomic.fna/checkm_input GCF_014280945.1_ASM1428094v1_genomic.fna/checkm_result
[2024-01-24 12:39:04,594] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:04,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:04,623] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:04,624] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:04,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014280945.1_ASM1428094v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:04,624] [INFO] Task started: Blastn
[2024-01-24 12:39:04,625] [INFO] Running command: blastn -query GCF_014280945.1_ASM1428094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237887c5-6888-4edf-967b-828d1c63ae43/dqc_reference/reference_markers_gtdb.fasta -out GCF_014280945.1_ASM1428094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:06,793] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:06,797] [INFO] Selected 12 target genomes.
[2024-01-24 12:39:06,798] [INFO] Target genome list was writen to GCF_014280945.1_ASM1428094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:06,807] [INFO] Task started: fastANI
[2024-01-24 12:39:06,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg1228ecf2-18ab-4399-bbc1-732a189fecc1/GCF_014280945.1_ASM1428094v1_genomic.fna.gz --refList GCF_014280945.1_ASM1428094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014280945.1_ASM1428094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:34,117] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:34,132] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:34,133] [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_000772045.1	s__Streptomyces sp000772045	95.89	2273	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	conclusive
GCF_003112555.1	s__Streptomyces coelicoflavus	93.3742	2251	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_003369795.1	s__Streptomyces sp003369795	92.8967	2022	2773	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	92.8167	2123	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_003112575.1	s__Streptomyces ardesiacus	92.8006	2061	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_002939385.1	s__Streptomyces sp002939385	92.7991	1976	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_003112595.1	s__Streptomyces rubrogriseus	92.7197	2131	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_014651155.1	s__Streptomyces anthocyanicus	92.6845	2139	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	-
GCA_000720845.1	s__Streptomyces sp000720845	92.5854	2086	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717995.1	s__Streptomyces violaceorubidus	92.4248	1952	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364245.1	s__Streptomyces sp004364245	92.0655	2026	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905385.1	s__Streptomyces sp001905385	89.9657	1987	2773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:34,135] [INFO] GTDB search result was written to GCF_014280945.1_ASM1428094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:34,136] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:34,144] [INFO] DFAST_QC result json was written to GCF_014280945.1_ASM1428094v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:34,145] [INFO] DFAST_QC completed!
[2024-01-24 12:39:34,145] [INFO] Total running time: 0h3m10s