[2024-01-24 10:57:38,700] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ef896a2-430b-46ba-9015-5e96d08f0a32/dqc_reference
[2024-01-24 10:57:40,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,038] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg977667fe-f71b-49f4-8c59-e2993d60c7ce/GCF_002154385.1_ASM215438v1_genomic.fna.gz | prodigal -d GCF_002154385.1_ASM215438v1_genomic.fna/cds.fna -a GCF_002154385.1_ASM215438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:57,708] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:57,709] [INFO] Task started: HMMsearch
[2024-01-24 10:57:57,709] [INFO] Running command: hmmsearch --tblout GCF_002154385.1_ASM215438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ef896a2-430b-46ba-9015-5e96d08f0a32/dqc_reference/reference_markers.hmm GCF_002154385.1_ASM215438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:58,035] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:58,036] [INFO] Found 6/6 markers.
[2024-01-24 10:57:58,094] [INFO] Query marker FASTA was written to GCF_002154385.1_ASM215438v1_genomic.fna/markers.fasta
[2024-01-24 10:57:58,094] [INFO] Task started: Blastn
[2024-01-24 10:57:58,094] [INFO] Running command: blastn -query GCF_002154385.1_ASM215438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ef896a2-430b-46ba-9015-5e96d08f0a32/dqc_reference/reference_markers.fasta -out GCF_002154385.1_ASM215438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:59,372] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:59,375] [INFO] Selected 13 target genomes.
[2024-01-24 10:57:59,376] [INFO] Target genome list was writen to GCF_002154385.1_ASM215438v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:59,382] [INFO] Task started: fastANI
[2024-01-24 10:57:59,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg977667fe-f71b-49f4-8c59-e2993d60c7ce/GCF_002154385.1_ASM215438v1_genomic.fna.gz --refList GCF_002154385.1_ASM215438v1_genomic.fna/target_genomes.txt --output GCF_002154385.1_ASM215438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:23,407] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:23,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ef896a2-430b-46ba-9015-5e96d08f0a32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:23,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ef896a2-430b-46ba-9015-5e96d08f0a32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:23,420] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:23,421] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:23,421] [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	94.8653	1758	2126	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	94.7253	1667	2126	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	94.2356	1692	2126	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	94.1042	1699	2126	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	92.1154	1770	2126	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	91.7275	1724	2126	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	90.7438	1667	2126	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	89.7112	1668	2126	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	89.0271	1359	2126	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.8207	1371	2126	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.9387	1236	2126	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.7038	1297	2126	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.5916	1216	2126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:23,422] [INFO] DFAST Taxonomy check result was written to GCF_002154385.1_ASM215438v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:23,423] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:23,423] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:23,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ef896a2-430b-46ba-9015-5e96d08f0a32/dqc_reference/checkm_data
[2024-01-24 10:58:23,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:23,492] [INFO] Task started: CheckM
[2024-01-24 10:58:23,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154385.1_ASM215438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154385.1_ASM215438v1_genomic.fna/checkm_input GCF_002154385.1_ASM215438v1_genomic.fna/checkm_result
[2024-01-24 10:59:18,006] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:18,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:18,035] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:18,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:18,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154385.1_ASM215438v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:18,037] [INFO] Task started: Blastn
[2024-01-24 10:59:18,037] [INFO] Running command: blastn -query GCF_002154385.1_ASM215438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ef896a2-430b-46ba-9015-5e96d08f0a32/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154385.1_ASM215438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:20,126] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:20,130] [INFO] Selected 8 target genomes.
[2024-01-24 10:59:20,130] [INFO] Target genome list was writen to GCF_002154385.1_ASM215438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:20,137] [INFO] Task started: fastANI
[2024-01-24 10:59:20,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg977667fe-f71b-49f4-8c59-e2993d60c7ce/GCF_002154385.1_ASM215438v1_genomic.fna.gz --refList GCF_002154385.1_ASM215438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154385.1_ASM215438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:35,223] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:35,238] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 10:59:35,239] [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
GCA_014649555.1	s__Streptomyces globisporus	99.2938	1965	2126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	inconclusive
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	96.2964	1805	2126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	inconclusive
GCF_003501885.1	s__Streptomyces globisporus_D	95.5523	1677	2126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_000718455.1	s__Streptomyces globisporus_A	94.9371	1736	2126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2621	N/A	N/A	N/A	N/A	1	-
GCF_014648875.1	s__Streptomyces parvus	94.8422	1760	2126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	-
GCF_001687325.1	s__Streptomyces sp001687325	94.5156	1718	2126	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	94.22	1693	2126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0775	95.83	95.78	0.85	0.84	5	-
GCF_016901035.1	s__Streptomyces sp016901035	94.1651	1669	2126	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 10:59:35,241] [INFO] GTDB search result was written to GCF_002154385.1_ASM215438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:35,241] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:35,246] [INFO] DFAST_QC result json was written to GCF_002154385.1_ASM215438v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:35,247] [INFO] DFAST_QC completed!
[2024-01-24 10:59:35,247] [INFO] Total running time: 0h1m57s