[2024-01-25 17:54:35,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:35,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:35,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg90b9557c-04f8-40ea-9edf-0406bcc03255/dqc_reference
[2024-01-25 17:54:36,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:36,759] [INFO] Task started: Prodigal
[2024-01-25 17:54:36,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg437d58d7-373d-4178-854e-e0c375831dbe/GCF_014649875.1_ASM1464987v1_genomic.fna.gz | prodigal -d GCF_014649875.1_ASM1464987v1_genomic.fna/cds.fna -a GCF_014649875.1_ASM1464987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:55,296] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:55,296] [INFO] Task started: HMMsearch
[2024-01-25 17:54:55,297] [INFO] Running command: hmmsearch --tblout GCF_014649875.1_ASM1464987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90b9557c-04f8-40ea-9edf-0406bcc03255/dqc_reference/reference_markers.hmm GCF_014649875.1_ASM1464987v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:55,624] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:55,625] [INFO] Found 6/6 markers.
[2024-01-25 17:54:55,680] [INFO] Query marker FASTA was written to GCF_014649875.1_ASM1464987v1_genomic.fna/markers.fasta
[2024-01-25 17:54:55,681] [INFO] Task started: Blastn
[2024-01-25 17:54:55,681] [INFO] Running command: blastn -query GCF_014649875.1_ASM1464987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90b9557c-04f8-40ea-9edf-0406bcc03255/dqc_reference/reference_markers.fasta -out GCF_014649875.1_ASM1464987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:56,913] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:56,916] [INFO] Selected 13 target genomes.
[2024-01-25 17:54:56,916] [INFO] Target genome list was writen to GCF_014649875.1_ASM1464987v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:56,923] [INFO] Task started: fastANI
[2024-01-25 17:54:56,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg437d58d7-373d-4178-854e-e0c375831dbe/GCF_014649875.1_ASM1464987v1_genomic.fna.gz --refList GCF_014649875.1_ASM1464987v1_genomic.fna/target_genomes.txt --output GCF_014649875.1_ASM1464987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:23,192] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:23,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90b9557c-04f8-40ea-9edf-0406bcc03255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:23,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90b9557c-04f8-40ea-9edf-0406bcc03255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:23,202] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:55:23,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:55:23,202] [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 parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	95.2155	2136	2495	95	conclusive
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	95.0932	1926	2495	95	conclusive
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	94.5756	2028	2495	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	94.4191	2027	2495	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	92.3775	2134	2495	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	91.9294	2088	2495	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	90.7456	2024	2495	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	89.8665	2017	2495	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	89.1495	1580	2495	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.8028	1596	2495	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.7581	1372	2495	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.551	1484	2495	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.3278	1208	2495	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:23,203] [INFO] DFAST Taxonomy check result was written to GCF_014649875.1_ASM1464987v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:23,204] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:23,204] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:23,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90b9557c-04f8-40ea-9edf-0406bcc03255/dqc_reference/checkm_data
[2024-01-25 17:55:23,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:23,270] [INFO] Task started: CheckM
[2024-01-25 17:55:23,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649875.1_ASM1464987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649875.1_ASM1464987v1_genomic.fna/checkm_input GCF_014649875.1_ASM1464987v1_genomic.fna/checkm_result
[2024-01-25 17:56:58,787] [INFO] Task succeeded: CheckM
[2024-01-25 17:56:58,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:56:58,812] [INFO] ===== Completeness check finished =====
[2024-01-25 17:56:58,813] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:56:58,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649875.1_ASM1464987v1_genomic.fna/markers.fasta)
[2024-01-25 17:56:58,815] [INFO] Task started: Blastn
[2024-01-25 17:56:58,815] [INFO] Running command: blastn -query GCF_014649875.1_ASM1464987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90b9557c-04f8-40ea-9edf-0406bcc03255/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649875.1_ASM1464987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:57:00,822] [INFO] Task succeeded: Blastn
[2024-01-25 17:57:00,827] [INFO] Selected 10 target genomes.
[2024-01-25 17:57:00,827] [INFO] Target genome list was writen to GCF_014649875.1_ASM1464987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:57:00,833] [INFO] Task started: fastANI
[2024-01-25 17:57:00,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg437d58d7-373d-4178-854e-e0c375831dbe/GCF_014649875.1_ASM1464987v1_genomic.fna.gz --refList GCF_014649875.1_ASM1464987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649875.1_ASM1464987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:57:21,253] [INFO] Task succeeded: fastANI
[2024-01-25 17:57:21,260] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:57:21,260] [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_014649875.1	s__Streptomyces rubiginosohelvolus	100.0	2493	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	conclusive
GCA_014649555.1	s__Streptomyces globisporus	96.2784	2225	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	-
GCF_003501885.1	s__Streptomyces globisporus_D	95.5696	1926	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_014648875.1	s__Streptomyces parvus	95.225	2135	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	-
GCF_000718455.1	s__Streptomyces globisporus_A	95.2151	2036	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2621	N/A	N/A	N/A	N/A	1	-
GCF_001687325.1	s__Streptomyces sp001687325	94.9891	2094	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649035.1	s__Streptomyces sindenensis	94.5737	2028	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0775	95.83	95.78	0.85	0.84	5	-
GCF_018866325.1	s__Streptomyces sp001895105	93.761	2031	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.85	98.85	0.87	0.87	2	-
GCA_002551355.1	s__Streptomyces sp002551355	93.4479	2101	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002154345.1	s__Streptomyces fimicarius	92.6729	1751	2495	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.88	95.22	0.89	0.81	11	-
--------------------------------------------------------------------------------
[2024-01-25 17:57:21,262] [INFO] GTDB search result was written to GCF_014649875.1_ASM1464987v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:57:21,263] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:57:21,266] [INFO] DFAST_QC result json was written to GCF_014649875.1_ASM1464987v1_genomic.fna/dqc_result.json
[2024-01-25 17:57:21,267] [INFO] DFAST_QC completed!
[2024-01-25 17:57:21,267] [INFO] Total running time: 0h2m46s