[2024-01-24 11:43:41,892] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:41,896] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:41,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bea03b6-4195-4260-afa3-84d8d80a95f8/dqc_reference
[2024-01-24 11:43:43,470] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,471] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,471] [INFO] Running command: gunzip -c /var/lib/cwl/stgccd12309-3eb5-40df-9f59-cd08cd82697b/GCF_002154345.1_ASM215434v1_genomic.fna.gz | prodigal -d GCF_002154345.1_ASM215434v1_genomic.fna/cds.fna -a GCF_002154345.1_ASM215434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:04,594] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:04,595] [INFO] Task started: HMMsearch
[2024-01-24 11:44:04,595] [INFO] Running command: hmmsearch --tblout GCF_002154345.1_ASM215434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bea03b6-4195-4260-afa3-84d8d80a95f8/dqc_reference/reference_markers.hmm GCF_002154345.1_ASM215434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:05,057] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:05,058] [INFO] Found 6/6 markers.
[2024-01-24 11:44:05,122] [INFO] Query marker FASTA was written to GCF_002154345.1_ASM215434v1_genomic.fna/markers.fasta
[2024-01-24 11:44:05,123] [INFO] Task started: Blastn
[2024-01-24 11:44:05,123] [INFO] Running command: blastn -query GCF_002154345.1_ASM215434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bea03b6-4195-4260-afa3-84d8d80a95f8/dqc_reference/reference_markers.fasta -out GCF_002154345.1_ASM215434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:06,535] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:06,539] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:06,539] [INFO] Target genome list was writen to GCF_002154345.1_ASM215434v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:06,550] [INFO] Task started: fastANI
[2024-01-24 11:44:06,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgccd12309-3eb5-40df-9f59-cd08cd82697b/GCF_002154345.1_ASM215434v1_genomic.fna.gz --refList GCF_002154345.1_ASM215434v1_genomic.fna/target_genomes.txt --output GCF_002154345.1_ASM215434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:35,979] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:35,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bea03b6-4195-4260-afa3-84d8d80a95f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:35,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bea03b6-4195-4260-afa3-84d8d80a95f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:35,992] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:35,992] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:35,992] [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 anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	92.5937	1867	2229	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	92.4059	1797	2229	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	92.3221	1705	2229	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	92.2571	1738	2229	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	92.0825	1724	2229	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	91.8535	1772	2229	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	91.8304	1758	2229	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	90.3565	1698	2229	95	below_threshold
Streptomyces californicus	strain=NRRL B-2098	GCA_000717645.1	67351	67351	type	True	90.332	1707	2229	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	89.764	1729	2229	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	88.9303	1430	2229	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.6682	1416	2229	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.5375	1299	2229	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.5066	1235	2229	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.2848	1169	2229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,994] [INFO] DFAST Taxonomy check result was written to GCF_002154345.1_ASM215434v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:35,994] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:35,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:35,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bea03b6-4195-4260-afa3-84d8d80a95f8/dqc_reference/checkm_data
[2024-01-24 11:44:35,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:36,070] [INFO] Task started: CheckM
[2024-01-24 11:44:36,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154345.1_ASM215434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154345.1_ASM215434v1_genomic.fna/checkm_input GCF_002154345.1_ASM215434v1_genomic.fna/checkm_result
[2024-01-24 11:45:41,095] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:41,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:41,126] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:41,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:41,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154345.1_ASM215434v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:41,127] [INFO] Task started: Blastn
[2024-01-24 11:45:41,127] [INFO] Running command: blastn -query GCF_002154345.1_ASM215434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bea03b6-4195-4260-afa3-84d8d80a95f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154345.1_ASM215434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:43,301] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:43,305] [INFO] Selected 15 target genomes.
[2024-01-24 11:45:43,306] [INFO] Target genome list was writen to GCF_002154345.1_ASM215434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:43,317] [INFO] Task started: fastANI
[2024-01-24 11:45:43,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgccd12309-3eb5-40df-9f59-cd08cd82697b/GCF_002154345.1_ASM215434v1_genomic.fna.gz --refList GCF_002154345.1_ASM215434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154345.1_ASM215434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:10,369] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:10,387] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:10,387] [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_002154345.1	s__Streptomyces fimicarius	100.0	2197	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.88	95.22	0.89	0.81	11	conclusive
GCF_001687325.1	s__Streptomyces sp001687325	92.7123	1800	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721175.1	s__Streptomyces anulatus_C	92.6906	1684	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.46	0.95	0.90	3	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	92.6434	1782	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCA_002551355.1	s__Streptomyces sp002551355	92.64	1746	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650675.1	s__Streptomyces anulatus	92.6126	1865	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.62	96.42	0.89	0.81	27	-
GCF_016901035.1	s__Streptomyces sp016901035	92.6114	1664	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003501885.1	s__Streptomyces globisporus_D	92.561	1650	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_002910905.1	s__Streptomyces sp002910905	92.5601	1618	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649555.1	s__Streptomyces globisporus	92.5027	1795	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	-
GCF_018619185.1	s__Streptomyces sp018619185	92.4998	1681	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718455.1	s__Streptomyces globisporus_A	92.2816	1706	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2621	N/A	N/A	N/A	N/A	1	-
GCF_900460065.1	s__Streptomyces griseus	91.8799	1753	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.49	99.03	0.95	0.93	10	-
GCF_018866325.1	s__Streptomyces sp001895105	91.483	1694	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.85	98.85	0.87	0.87	2	-
GCF_014650075.1	s__Streptomyces microflavus	89.7448	1731	2229	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.25	97.27	0.91	0.85	13	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:10,389] [INFO] GTDB search result was written to GCF_002154345.1_ASM215434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:10,390] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:10,393] [INFO] DFAST_QC result json was written to GCF_002154345.1_ASM215434v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:10,393] [INFO] DFAST_QC completed!
[2024-01-24 11:46:10,394] [INFO] Total running time: 0h2m29s