[2024-01-24 14:10:15,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:15,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:15,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg65dbdd3d-da9b-405a-ab4f-0b70fd5f35d7/dqc_reference
[2024-01-24 14:10:16,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:16,753] [INFO] Task started: Prodigal
[2024-01-24 14:10:16,753] [INFO] Running command: gunzip -c /var/lib/cwl/stga514922a-7a5d-4c91-85d1-37deef302076/GCF_008369065.1_ASM836906v1_genomic.fna.gz | prodigal -d GCF_008369065.1_ASM836906v1_genomic.fna/cds.fna -a GCF_008369065.1_ASM836906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:45,207] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:45,207] [INFO] Task started: HMMsearch
[2024-01-24 14:10:45,207] [INFO] Running command: hmmsearch --tblout GCF_008369065.1_ASM836906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65dbdd3d-da9b-405a-ab4f-0b70fd5f35d7/dqc_reference/reference_markers.hmm GCF_008369065.1_ASM836906v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:45,570] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:45,571] [INFO] Found 6/6 markers.
[2024-01-24 14:10:45,637] [INFO] Query marker FASTA was written to GCF_008369065.1_ASM836906v1_genomic.fna/markers.fasta
[2024-01-24 14:10:45,637] [INFO] Task started: Blastn
[2024-01-24 14:10:45,638] [INFO] Running command: blastn -query GCF_008369065.1_ASM836906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65dbdd3d-da9b-405a-ab4f-0b70fd5f35d7/dqc_reference/reference_markers.fasta -out GCF_008369065.1_ASM836906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:47,029] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:47,033] [INFO] Selected 21 target genomes.
[2024-01-24 14:10:47,033] [INFO] Target genome list was writen to GCF_008369065.1_ASM836906v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:47,042] [INFO] Task started: fastANI
[2024-01-24 14:10:47,042] [INFO] Running command: fastANI --query /var/lib/cwl/stga514922a-7a5d-4c91-85d1-37deef302076/GCF_008369065.1_ASM836906v1_genomic.fna.gz --refList GCF_008369065.1_ASM836906v1_genomic.fna/target_genomes.txt --output GCF_008369065.1_ASM836906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:11:33,078] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:33,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65dbdd3d-da9b-405a-ab4f-0b70fd5f35d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:11:33,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65dbdd3d-da9b-405a-ab4f-0b70fd5f35d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:11:33,095] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:11:33,095] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:11:33,095] [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 aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	89.0442	1889	2814	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	87.6253	2045	2814	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	87.5044	1838	2814	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.4481	1874	2814	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	85.1304	1762	2814	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.9574	1718	2814	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.8742	1587	2814	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.8429	1725	2814	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000968255.1	33903	33903	type	True	84.722	1772	2814	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.698	1788	2814	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	84.6062	1827	2814	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	84.5653	1834	2814	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	83.9599	1662	2814	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.8878	1762	2814	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	83.8656	1364	2814	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.8128	1551	2814	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	83.7938	1666	2814	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	83.7881	1696	2814	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.6918	1805	2814	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	83.674	1700	2814	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	83.1511	1436	2814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:11:33,097] [INFO] DFAST Taxonomy check result was written to GCF_008369065.1_ASM836906v1_genomic.fna/tc_result.tsv
[2024-01-24 14:11:33,097] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:11:33,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:11:33,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65dbdd3d-da9b-405a-ab4f-0b70fd5f35d7/dqc_reference/checkm_data
[2024-01-24 14:11:33,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:11:33,200] [INFO] Task started: CheckM
[2024-01-24 14:11:33,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008369065.1_ASM836906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008369065.1_ASM836906v1_genomic.fna/checkm_input GCF_008369065.1_ASM836906v1_genomic.fna/checkm_result
[2024-01-24 14:12:46,564] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:46,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:46,596] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:46,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:46,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008369065.1_ASM836906v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:46,597] [INFO] Task started: Blastn
[2024-01-24 14:12:46,597] [INFO] Running command: blastn -query GCF_008369065.1_ASM836906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65dbdd3d-da9b-405a-ab4f-0b70fd5f35d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_008369065.1_ASM836906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:48,709] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:48,714] [INFO] Selected 11 target genomes.
[2024-01-24 14:12:48,714] [INFO] Target genome list was writen to GCF_008369065.1_ASM836906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:48,742] [INFO] Task started: fastANI
[2024-01-24 14:12:48,743] [INFO] Running command: fastANI --query /var/lib/cwl/stga514922a-7a5d-4c91-85d1-37deef302076/GCF_008369065.1_ASM836906v1_genomic.fna.gz --refList GCF_008369065.1_ASM836906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008369065.1_ASM836906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:17,037] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:17,047] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:17,047] [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_008369065.1	s__Streptomyces sp008369065	100.0	2807	2814	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_018070025.1	s__Streptomyces sp018070025	89.6489	2278	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650955.1	s__Streptomyces tauricus	89.5837	2173	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024195.1	s__Streptomyces dioscori	89.4924	2259	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418335.1	s__Streptomyces aurantiacus	89.0695	1885	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_019090165.1	s__Streptomyces sp019090165	88.681	1970	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050945.1	s__Streptomyces sp007050945	87.6453	2045	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	87.5225	2050	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	87.2518	1927	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651055.1	s__Streptomyces fructofermentans	86.4153	1879	2814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664315.1	s__Streptomyces sp003664315	84.7473	1771	2814	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 14:13:17,049] [INFO] GTDB search result was written to GCF_008369065.1_ASM836906v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:17,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:17,055] [INFO] DFAST_QC result json was written to GCF_008369065.1_ASM836906v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:17,055] [INFO] DFAST_QC completed!
[2024-01-24 14:13:17,055] [INFO] Total running time: 0h3m2s