[2024-01-24 13:10:03,119] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a18ad52-e207-4e39-8eb6-05fd21ee71f2/dqc_reference
[2024-01-24 13:10:04,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:04,459] [INFO] Task started: Prodigal
[2024-01-24 13:10:04,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg78ec58c0-b48e-4166-86c4-66c9d30579de/GCF_008704495.1_ASM870449v1_genomic.fna.gz | prodigal -d GCF_008704495.1_ASM870449v1_genomic.fna/cds.fna -a GCF_008704495.1_ASM870449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:38,458] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:38,458] [INFO] Task started: HMMsearch
[2024-01-24 13:10:38,459] [INFO] Running command: hmmsearch --tblout GCF_008704495.1_ASM870449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a18ad52-e207-4e39-8eb6-05fd21ee71f2/dqc_reference/reference_markers.hmm GCF_008704495.1_ASM870449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:38,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:38,953] [INFO] Found 6/6 markers.
[2024-01-24 13:10:39,033] [INFO] Query marker FASTA was written to GCF_008704495.1_ASM870449v1_genomic.fna/markers.fasta
[2024-01-24 13:10:39,033] [INFO] Task started: Blastn
[2024-01-24 13:10:39,033] [INFO] Running command: blastn -query GCF_008704495.1_ASM870449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a18ad52-e207-4e39-8eb6-05fd21ee71f2/dqc_reference/reference_markers.fasta -out GCF_008704495.1_ASM870449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:40,371] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:40,375] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:40,376] [INFO] Target genome list was writen to GCF_008704495.1_ASM870449v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:40,390] [INFO] Task started: fastANI
[2024-01-24 13:10:40,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg78ec58c0-b48e-4166-86c4-66c9d30579de/GCF_008704495.1_ASM870449v1_genomic.fna.gz --refList GCF_008704495.1_ASM870449v1_genomic.fna/target_genomes.txt --output GCF_008704495.1_ASM870449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:11:12,416] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:12,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a18ad52-e207-4e39-8eb6-05fd21ee71f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:11:12,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a18ad52-e207-4e39-8eb6-05fd21ee71f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:11:12,440] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:11:12,440] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:11:12,441] [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 kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	100.0	3375	3377	95	conclusive
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	99.827	2819	3377	95	conclusive
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	88.3951	1999	3377	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	88.142	1994	3377	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	87.6805	1667	3377	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	87.6431	2010	3377	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	86.8368	1852	3377	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	85.9317	2213	3377	95	below_threshold
Streptomyces longisporoflavus	strain=JCM 4396	GCA_014649775.1	28044	28044	type	True	85.6483	2029	3377	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	84.2941	2098	3377	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	82.6484	1427	3377	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	82.3492	1708	3377	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	81.8904	1562	3377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:11:12,443] [INFO] DFAST Taxonomy check result was written to GCF_008704495.1_ASM870449v1_genomic.fna/tc_result.tsv
[2024-01-24 13:11:12,443] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:11:12,443] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:11:12,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a18ad52-e207-4e39-8eb6-05fd21ee71f2/dqc_reference/checkm_data
[2024-01-24 13:11:12,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:11:12,542] [INFO] Task started: CheckM
[2024-01-24 13:11:12,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704495.1_ASM870449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704495.1_ASM870449v1_genomic.fna/checkm_input GCF_008704495.1_ASM870449v1_genomic.fna/checkm_result
[2024-01-24 13:13:39,580] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:39,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:39,605] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:39,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:39,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704495.1_ASM870449v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:39,605] [INFO] Task started: Blastn
[2024-01-24 13:13:39,606] [INFO] Running command: blastn -query GCF_008704495.1_ASM870449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a18ad52-e207-4e39-8eb6-05fd21ee71f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704495.1_ASM870449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:41,968] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:41,972] [INFO] Selected 12 target genomes.
[2024-01-24 13:13:41,973] [INFO] Target genome list was writen to GCF_008704495.1_ASM870449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:42,013] [INFO] Task started: fastANI
[2024-01-24 13:13:42,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg78ec58c0-b48e-4166-86c4-66c9d30579de/GCF_008704495.1_ASM870449v1_genomic.fna.gz --refList GCF_008704495.1_ASM870449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704495.1_ASM870449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:14,172] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:14,184] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:14,185] [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_008704495.1	s__Streptomyces kanamyceticus	100.0	3375	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	conclusive
GCF_002556545.1	s__Streptomyces formicae	94.3637	2787	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419745.1	s__Streptomyces silaceus	88.3779	2001	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.58	0.96	0.96	2	-
GCF_001418325.1	s__Streptomyces atriruber	88.1781	1990	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945545.1	s__Streptomyces sp003945545	87.774	2023	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642335.1	s__Streptomyces venezuelae_F	87.7612	2152	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704395.1	s__Streptomyces alboniger	87.6551	2010	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.40	96.83	0.93	0.87	3	-
GCF_008642315.1	s__Streptomyces venezuelae_D	87.6034	2257	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642355.1	s__Streptomyces venezuelae_B	87.437	2105	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.56	0.88	0.87	4	-
GCA_004010275.1	s__Streptomyces huasconensis	87.3939	1803	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684775.1	s__Streptomyces sp004684775	86.3129	1809	3377	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649775.1	s__Streptomyces longisporoflavus	85.6206	2035	3377	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 13:14:14,187] [INFO] GTDB search result was written to GCF_008704495.1_ASM870449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:14,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:14,191] [INFO] DFAST_QC result json was written to GCF_008704495.1_ASM870449v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:14,191] [INFO] DFAST_QC completed!
[2024-01-24 13:14:14,191] [INFO] Total running time: 0h4m11s