[2024-01-24 11:58:56,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:56,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:56,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg309ee25a-4961-48ad-a15b-a5754871f46d/dqc_reference
[2024-01-24 11:58:57,470] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:57,472] [INFO] Task started: Prodigal
[2024-01-24 11:58:57,472] [INFO] Running command: gunzip -c /var/lib/cwl/stga445130e-2e59-4496-9bb0-45a83b93f7a8/GCF_016598475.1_ASM1659847v1_genomic.fna.gz | prodigal -d GCF_016598475.1_ASM1659847v1_genomic.fna/cds.fna -a GCF_016598475.1_ASM1659847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:23,317] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:23,318] [INFO] Task started: HMMsearch
[2024-01-24 11:59:23,318] [INFO] Running command: hmmsearch --tblout GCF_016598475.1_ASM1659847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg309ee25a-4961-48ad-a15b-a5754871f46d/dqc_reference/reference_markers.hmm GCF_016598475.1_ASM1659847v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:23,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:23,766] [INFO] Found 6/6 markers.
[2024-01-24 11:59:23,830] [INFO] Query marker FASTA was written to GCF_016598475.1_ASM1659847v1_genomic.fna/markers.fasta
[2024-01-24 11:59:23,830] [INFO] Task started: Blastn
[2024-01-24 11:59:23,830] [INFO] Running command: blastn -query GCF_016598475.1_ASM1659847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309ee25a-4961-48ad-a15b-a5754871f46d/dqc_reference/reference_markers.fasta -out GCF_016598475.1_ASM1659847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:25,029] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:25,033] [INFO] Selected 21 target genomes.
[2024-01-24 11:59:25,033] [INFO] Target genome list was writen to GCF_016598475.1_ASM1659847v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:25,055] [INFO] Task started: fastANI
[2024-01-24 11:59:25,056] [INFO] Running command: fastANI --query /var/lib/cwl/stga445130e-2e59-4496-9bb0-45a83b93f7a8/GCF_016598475.1_ASM1659847v1_genomic.fna.gz --refList GCF_016598475.1_ASM1659847v1_genomic.fna/target_genomes.txt --output GCF_016598475.1_ASM1659847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:15,369] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:15,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg309ee25a-4961-48ad-a15b-a5754871f46d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:15,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg309ee25a-4961-48ad-a15b-a5754871f46d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:15,385] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:15,385] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:15,385] [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 adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	100.0	2943	2958	95	conclusive
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	89.2209	2098	2958	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	89.2168	2216	2958	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	89.1893	2209	2958	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	89.0967	2109	2958	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	89.0497	2115	2958	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	88.9942	2248	2958	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	88.7716	2143	2958	95	below_threshold
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	88.5531	2121	2958	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	88.4341	2134	2958	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.7534	1704	2958	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.5371	2073	2958	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.4475	1880	2958	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.2583	1919	2958	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	83.9714	1813	2958	95	below_threshold
Streptomyces lacrimifluminis	strain=CGMCC 4.7272	GCA_014646095.1	1500077	1500077	type	True	83.8821	1814	2958	95	below_threshold
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	83.7711	1784	2958	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	83.6727	1541	2958	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	83.6657	1832	2958	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	83.2517	1693	2958	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	79.5521	856	2958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:15,387] [INFO] DFAST Taxonomy check result was written to GCF_016598475.1_ASM1659847v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:15,387] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:15,388] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:15,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg309ee25a-4961-48ad-a15b-a5754871f46d/dqc_reference/checkm_data
[2024-01-24 12:00:15,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:15,470] [INFO] Task started: CheckM
[2024-01-24 12:00:15,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016598475.1_ASM1659847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016598475.1_ASM1659847v1_genomic.fna/checkm_input GCF_016598475.1_ASM1659847v1_genomic.fna/checkm_result
[2024-01-24 12:01:39,882] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:39,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:39,904] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:39,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:39,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016598475.1_ASM1659847v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:39,905] [INFO] Task started: Blastn
[2024-01-24 12:01:39,905] [INFO] Running command: blastn -query GCF_016598475.1_ASM1659847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309ee25a-4961-48ad-a15b-a5754871f46d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016598475.1_ASM1659847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:41,766] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:41,769] [INFO] Selected 18 target genomes.
[2024-01-24 12:01:41,770] [INFO] Target genome list was writen to GCF_016598475.1_ASM1659847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:41,794] [INFO] Task started: fastANI
[2024-01-24 12:01:41,795] [INFO] Running command: fastANI --query /var/lib/cwl/stga445130e-2e59-4496-9bb0-45a83b93f7a8/GCF_016598475.1_ASM1659847v1_genomic.fna.gz --refList GCF_016598475.1_ASM1659847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016598475.1_ASM1659847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:23,131] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:23,145] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:23,145] [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_016598475.1	s__Streptomyces adelaidensis	100.0	2943	2958	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_001550375.1	s__Streptomyces europaeiscabiei	89.7527	1964	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	89.2342	2213	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018927715.1	s__Streptomyces brasiliscabiei	89.2124	2100	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772895.1	s__Streptomyces galbus_A	89.152	2216	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383595.1	s__Streptomyces bottropensis	89.0775	2111	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_900114955.1	s__Streptomyces sp900114955	89.0365	2212	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	-
GCF_014873495.1	s__Streptomyces stelliscabiei	89.0216	2168	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_014203845.1	s__Streptomyces scabiei_E	88.809	2100	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_008386495.1	s__Streptomyces tailanensis	88.7828	2141	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214185.1	s__Streptomyces capitiformicae	88.455	2131	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	1.00	1.00	2	-
GCF_000718165.1	s__Streptomyces fulvoviolaceus	84.499	1934	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	84.4721	1876	2958	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	84.2816	1884	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648915.1	s__Streptomyces phaeofaciens	83.9844	1810	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377175.1	s__Streptomyces adustus	83.6882	1538	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222485.1	s__Streptomyces griseoviridis_A	83.3421	1629	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900091845.1	s__Streptomyces sp900091845	83.1495	1544	2958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:23,147] [INFO] GTDB search result was written to GCF_016598475.1_ASM1659847v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:23,147] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:23,152] [INFO] DFAST_QC result json was written to GCF_016598475.1_ASM1659847v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:23,152] [INFO] DFAST_QC completed!
[2024-01-24 12:02:23,152] [INFO] Total running time: 0h3m27s