[2024-01-24 14:54:56,705] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,706] [INFO] DQC Reference Directory: /var/lib/cwl/stga43ce7dd-5100-45a2-96eb-984626a7a802/dqc_reference
[2024-01-24 14:54:58,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:58,099] [INFO] Task started: Prodigal
[2024-01-24 14:54:58,099] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf9b82e4-3f46-4a2d-bf31-59aea95c9041/GCF_002954775.1_ASM295477v1_genomic.fna.gz | prodigal -d GCF_002954775.1_ASM295477v1_genomic.fna/cds.fna -a GCF_002954775.1_ASM295477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:27,235] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:27,236] [INFO] Task started: HMMsearch
[2024-01-24 14:55:27,236] [INFO] Running command: hmmsearch --tblout GCF_002954775.1_ASM295477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga43ce7dd-5100-45a2-96eb-984626a7a802/dqc_reference/reference_markers.hmm GCF_002954775.1_ASM295477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:27,722] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:27,724] [INFO] Found 6/6 markers.
[2024-01-24 14:55:27,807] [INFO] Query marker FASTA was written to GCF_002954775.1_ASM295477v1_genomic.fna/markers.fasta
[2024-01-24 14:55:27,808] [INFO] Task started: Blastn
[2024-01-24 14:55:27,808] [INFO] Running command: blastn -query GCF_002954775.1_ASM295477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga43ce7dd-5100-45a2-96eb-984626a7a802/dqc_reference/reference_markers.fasta -out GCF_002954775.1_ASM295477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:29,144] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:29,148] [INFO] Selected 18 target genomes.
[2024-01-24 14:55:29,148] [INFO] Target genome list was writen to GCF_002954775.1_ASM295477v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:29,158] [INFO] Task started: fastANI
[2024-01-24 14:55:29,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf9b82e4-3f46-4a2d-bf31-59aea95c9041/GCF_002954775.1_ASM295477v1_genomic.fna.gz --refList GCF_002954775.1_ASM295477v1_genomic.fna/target_genomes.txt --output GCF_002954775.1_ASM295477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:10,994] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:10,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga43ce7dd-5100-45a2-96eb-984626a7a802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:10,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga43ce7dd-5100-45a2-96eb-984626a7a802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:11,014] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:11,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:11,015] [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 geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	100.0	3345	3349	95	conclusive
Streptomyces lacrimifluminis	strain=CGMCC 4.7272	GCA_014646095.1	1500077	1500077	type	True	89.5653	2054	3349	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.4837	1966	3349	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.2928	1620	3349	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.2007	1682	3349	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.1102	1704	3349	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	83.9454	1797	3349	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	83.9145	1760	3349	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.9106	1898	3349	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	83.8573	1989	3349	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.8211	1923	3349	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	83.7229	1776	3349	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	83.5201	1531	3349	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	83.4117	1576	3349	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	83.3724	1621	3349	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	83.1824	1624	3349	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	81.604	1317	3349	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	81.5888	1494	3349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:11,017] [INFO] DFAST Taxonomy check result was written to GCF_002954775.1_ASM295477v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:11,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:11,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:11,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga43ce7dd-5100-45a2-96eb-984626a7a802/dqc_reference/checkm_data
[2024-01-24 14:56:11,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:11,113] [INFO] Task started: CheckM
[2024-01-24 14:56:11,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954775.1_ASM295477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954775.1_ASM295477v1_genomic.fna/checkm_input GCF_002954775.1_ASM295477v1_genomic.fna/checkm_result
[2024-01-24 14:57:40,606] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:40,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:40,638] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:40,639] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:40,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954775.1_ASM295477v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:40,640] [INFO] Task started: Blastn
[2024-01-24 14:57:40,640] [INFO] Running command: blastn -query GCF_002954775.1_ASM295477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga43ce7dd-5100-45a2-96eb-984626a7a802/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954775.1_ASM295477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:42,760] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:42,763] [INFO] Selected 9 target genomes.
[2024-01-24 14:57:42,764] [INFO] Target genome list was writen to GCF_002954775.1_ASM295477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:42,770] [INFO] Task started: fastANI
[2024-01-24 14:57:42,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf9b82e4-3f46-4a2d-bf31-59aea95c9041/GCF_002954775.1_ASM295477v1_genomic.fna.gz --refList GCF_002954775.1_ASM295477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954775.1_ASM295477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:08,028] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:08,038] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:08,038] [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_002954775.1	s__Streptomyces geranii	100.0	3345	3349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010548275.1	s__Streptomyces sp010548275	89.7292	2161	3349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646095.1	s__Streptomyces lacrimifluminis	89.527	2061	3349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331005.1	s__Streptomyces turgidiscabies	89.36	2090	3349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.67	0.92	0.88	3	-
GCF_001280005.1	s__Streptomyces sp001280005	89.0337	1917	3349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418565.1	s__Streptomyces graminilatus	88.7657	1638	3349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746395.1	s__Streptomyces mirabilis_A	84.526	1926	3349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012273535.1	s__Streptomyces sp002846625	83.833	1872	3349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4492	97.43	96.23	0.83	0.78	4	-
GCF_014645835.1	s__Streptomyces albiflavescens	83.7179	1778	3349	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 14:58:08,040] [INFO] GTDB search result was written to GCF_002954775.1_ASM295477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:08,041] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:08,045] [INFO] DFAST_QC result json was written to GCF_002954775.1_ASM295477v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:08,045] [INFO] DFAST_QC completed!
[2024-01-24 14:58:08,045] [INFO] Total running time: 0h3m11s