[2024-01-25 19:05:35,537] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:35,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:35,539] [INFO] DQC Reference Directory: /var/lib/cwl/stg60ed8386-4a1c-4145-835a-e0daa1957db6/dqc_reference
[2024-01-25 19:05:36,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:36,704] [INFO] Task started: Prodigal
[2024-01-25 19:05:36,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e7af0d7-4437-4bcb-b026-1c9e62171601/GCF_014645835.1_ASM1464583v1_genomic.fna.gz | prodigal -d GCF_014645835.1_ASM1464583v1_genomic.fna/cds.fna -a GCF_014645835.1_ASM1464583v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:04,540] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:04,540] [INFO] Task started: HMMsearch
[2024-01-25 19:06:04,540] [INFO] Running command: hmmsearch --tblout GCF_014645835.1_ASM1464583v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60ed8386-4a1c-4145-835a-e0daa1957db6/dqc_reference/reference_markers.hmm GCF_014645835.1_ASM1464583v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:04,967] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:04,968] [INFO] Found 6/6 markers.
[2024-01-25 19:06:05,047] [INFO] Query marker FASTA was written to GCF_014645835.1_ASM1464583v1_genomic.fna/markers.fasta
[2024-01-25 19:06:05,047] [INFO] Task started: Blastn
[2024-01-25 19:06:05,047] [INFO] Running command: blastn -query GCF_014645835.1_ASM1464583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60ed8386-4a1c-4145-835a-e0daa1957db6/dqc_reference/reference_markers.fasta -out GCF_014645835.1_ASM1464583v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:06,247] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:06,255] [INFO] Selected 14 target genomes.
[2024-01-25 19:06:06,255] [INFO] Target genome list was writen to GCF_014645835.1_ASM1464583v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:06,262] [INFO] Task started: fastANI
[2024-01-25 19:06:06,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7af0d7-4437-4bcb-b026-1c9e62171601/GCF_014645835.1_ASM1464583v1_genomic.fna.gz --refList GCF_014645835.1_ASM1464583v1_genomic.fna/target_genomes.txt --output GCF_014645835.1_ASM1464583v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:43,630] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:43,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60ed8386-4a1c-4145-835a-e0daa1957db6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:43,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60ed8386-4a1c-4145-835a-e0daa1957db6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:43,639] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:06:43,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:43,640] [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 albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	100.0	3604	3604	95	conclusive
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	89.1843	2010	3604	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	87.6361	2395	3604	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	87.4758	2392	3604	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	86.441	2033	3604	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	86.4407	2076	3604	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	86.4247	2040	3604	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	86.3897	2079	3604	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	86.3309	2149	3604	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.406	2135	3604	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	84.3429	1624	3604	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.0681	1825	3604	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.6922	1947	3604	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.4968	1955	3604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:43,641] [INFO] DFAST Taxonomy check result was written to GCF_014645835.1_ASM1464583v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:43,642] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:43,642] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:43,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60ed8386-4a1c-4145-835a-e0daa1957db6/dqc_reference/checkm_data
[2024-01-25 19:06:43,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:43,740] [INFO] Task started: CheckM
[2024-01-25 19:06:43,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645835.1_ASM1464583v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645835.1_ASM1464583v1_genomic.fna/checkm_input GCF_014645835.1_ASM1464583v1_genomic.fna/checkm_result
[2024-01-25 19:08:47,871] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:47,872] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 85.71%
--------------------------------------------------------------------------------
[2024-01-25 19:08:47,894] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:47,894] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:47,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645835.1_ASM1464583v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:47,895] [INFO] Task started: Blastn
[2024-01-25 19:08:47,895] [INFO] Running command: blastn -query GCF_014645835.1_ASM1464583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60ed8386-4a1c-4145-835a-e0daa1957db6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645835.1_ASM1464583v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:49,894] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:49,897] [INFO] Selected 10 target genomes.
[2024-01-25 19:08:49,897] [INFO] Target genome list was writen to GCF_014645835.1_ASM1464583v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:49,935] [INFO] Task started: fastANI
[2024-01-25 19:08:49,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7af0d7-4437-4bcb-b026-1c9e62171601/GCF_014645835.1_ASM1464583v1_genomic.fna.gz --refList GCF_014645835.1_ASM1464583v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645835.1_ASM1464583v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:18,564] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:18,571] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:18,571] [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_014645835.1	s__Streptomyces albiflavescens	100.0	3604	3604	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_002946835.1	s__Streptomyces dengpaensis	89.1699	2012	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002300165.1	s__Streptomyces sp002300165	88.2919	2269	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.35	96.35	0.87	0.87	2	-
GCF_014650275.1	s__Streptomyces mirabilis	87.6222	2398	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	96.82	96.27	0.84	0.80	23	-
GCF_012273535.1	s__Streptomyces sp002846625	87.5322	2416	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4492	97.43	96.23	0.83	0.78	4	-
GCF_001514115.1	s__Streptomyces olivochromogenes	87.4738	2391	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_012273515.1	s__Streptomyces sp012273515	86.604	2145	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009765.2	s__Streptomyces avermitilis	86.3825	2080	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.91	0.98	0.92	9	-
GCF_008905045.1	s__Streptomyces albicerus	85.3367	2212	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369065.1	s__Streptomyces sp008369065	84.3575	1812	3604	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:18,573] [INFO] GTDB search result was written to GCF_014645835.1_ASM1464583v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:18,574] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:18,577] [INFO] DFAST_QC result json was written to GCF_014645835.1_ASM1464583v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:18,577] [INFO] DFAST_QC completed!
[2024-01-25 19:09:18,577] [INFO] Total running time: 0h3m43s