[2024-01-24 13:19:26,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:26,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:26,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg7acd5e26-39c0-449e-97e8-dad8f8354398/dqc_reference
[2024-01-24 13:19:27,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,894] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg863d5dc1-2436-4205-a48c-78200425cdaa/GCF_014650955.1_ASM1465095v1_genomic.fna.gz | prodigal -d GCF_014650955.1_ASM1465095v1_genomic.fna/cds.fna -a GCF_014650955.1_ASM1465095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:54,768] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:54,769] [INFO] Task started: HMMsearch
[2024-01-24 13:19:54,769] [INFO] Running command: hmmsearch --tblout GCF_014650955.1_ASM1465095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7acd5e26-39c0-449e-97e8-dad8f8354398/dqc_reference/reference_markers.hmm GCF_014650955.1_ASM1465095v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:55,138] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:55,140] [INFO] Found 6/6 markers.
[2024-01-24 13:19:55,210] [INFO] Query marker FASTA was written to GCF_014650955.1_ASM1465095v1_genomic.fna/markers.fasta
[2024-01-24 13:19:55,211] [INFO] Task started: Blastn
[2024-01-24 13:19:55,211] [INFO] Running command: blastn -query GCF_014650955.1_ASM1465095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7acd5e26-39c0-449e-97e8-dad8f8354398/dqc_reference/reference_markers.fasta -out GCF_014650955.1_ASM1465095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:56,469] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:56,473] [INFO] Selected 21 target genomes.
[2024-01-24 13:19:56,474] [INFO] Target genome list was writen to GCF_014650955.1_ASM1465095v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:56,559] [INFO] Task started: fastANI
[2024-01-24 13:19:56,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg863d5dc1-2436-4205-a48c-78200425cdaa/GCF_014650955.1_ASM1465095v1_genomic.fna.gz --refList GCF_014650955.1_ASM1465095v1_genomic.fna/target_genomes.txt --output GCF_014650955.1_ASM1465095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:42,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:42,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7acd5e26-39c0-449e-97e8-dad8f8354398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:42,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7acd5e26-39c0-449e-97e8-dad8f8354398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:42,533] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:20:42,533] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:20:42,533] [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	90.0294	1979	3190	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	88.2787	2341	3190	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	88.0911	2119	3190	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.223	2055	3190	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	85.4176	1874	3190	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.6931	1883	3190	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.6897	1697	3190	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.6265	1910	3190	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	84.5806	2037	3190	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.5291	1968	3190	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	84.4342	1982	3190	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	83.7842	1806	3190	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.7101	1619	3190	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.7069	1961	3190	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.5052	1902	3190	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	83.2966	1730	3190	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	83.2797	1704	3190	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.8092	1498	3190	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	82.598	1520	3190	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.5481	1791	3190	95	below_threshold
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	82.1555	1331	3190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:42,535] [INFO] DFAST Taxonomy check result was written to GCF_014650955.1_ASM1465095v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:42,536] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:42,536] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:42,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7acd5e26-39c0-449e-97e8-dad8f8354398/dqc_reference/checkm_data
[2024-01-24 13:20:42,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:42,623] [INFO] Task started: CheckM
[2024-01-24 13:20:42,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650955.1_ASM1465095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650955.1_ASM1465095v1_genomic.fna/checkm_input GCF_014650955.1_ASM1465095v1_genomic.fna/checkm_result
[2024-01-24 13:22:10,020] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:10,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:10,046] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:10,046] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:10,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650955.1_ASM1465095v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:10,048] [INFO] Task started: Blastn
[2024-01-24 13:22:10,049] [INFO] Running command: blastn -query GCF_014650955.1_ASM1465095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7acd5e26-39c0-449e-97e8-dad8f8354398/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650955.1_ASM1465095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:12,118] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:12,123] [INFO] Selected 9 target genomes.
[2024-01-24 13:22:12,123] [INFO] Target genome list was writen to GCF_014650955.1_ASM1465095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:12,184] [INFO] Task started: fastANI
[2024-01-24 13:22:12,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg863d5dc1-2436-4205-a48c-78200425cdaa/GCF_014650955.1_ASM1465095v1_genomic.fna.gz --refList GCF_014650955.1_ASM1465095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650955.1_ASM1465095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:37,450] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:37,463] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:37,464] [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_014650955.1	s__Streptomyces tauricus	100.0	3182	3190	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	93.5212	2716	3190	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	93.5145	2702	3190	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	90.0266	1979	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_008369065.1	s__Streptomyces sp008369065	89.5898	2189	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090165.1	s__Streptomyces sp019090165	89.3774	2205	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	88.08	2121	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_008905045.1	s__Streptomyces albicerus	87.8818	2200	3190	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	86.1904	2060	3190	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 13:22:37,465] [INFO] GTDB search result was written to GCF_014650955.1_ASM1465095v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:37,466] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:37,469] [INFO] DFAST_QC result json was written to GCF_014650955.1_ASM1465095v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:37,469] [INFO] DFAST_QC completed!
[2024-01-24 13:22:37,470] [INFO] Total running time: 0h3m11s