[2024-01-25 18:04:35,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:35,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:35,656] [INFO] DQC Reference Directory: /var/lib/cwl/stgc67f4fa2-4684-4577-9716-a7f888766dda/dqc_reference
[2024-01-25 18:04:36,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:36,817] [INFO] Task started: Prodigal
[2024-01-25 18:04:36,818] [INFO] Running command: gunzip -c /var/lib/cwl/stge3dd1090-606a-4174-ac39-dbe5dd58cbab/GCF_030262575.1_ASM3026257v1_genomic.fna.gz | prodigal -d GCF_030262575.1_ASM3026257v1_genomic.fna/cds.fna -a GCF_030262575.1_ASM3026257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:05:00,969] [INFO] Task succeeded: Prodigal
[2024-01-25 18:05:00,969] [INFO] Task started: HMMsearch
[2024-01-25 18:05:00,969] [INFO] Running command: hmmsearch --tblout GCF_030262575.1_ASM3026257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc67f4fa2-4684-4577-9716-a7f888766dda/dqc_reference/reference_markers.hmm GCF_030262575.1_ASM3026257v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:05:01,381] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:05:01,382] [INFO] Found 6/6 markers.
[2024-01-25 18:05:01,446] [INFO] Query marker FASTA was written to GCF_030262575.1_ASM3026257v1_genomic.fna/markers.fasta
[2024-01-25 18:05:01,446] [INFO] Task started: Blastn
[2024-01-25 18:05:01,446] [INFO] Running command: blastn -query GCF_030262575.1_ASM3026257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc67f4fa2-4684-4577-9716-a7f888766dda/dqc_reference/reference_markers.fasta -out GCF_030262575.1_ASM3026257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:02,743] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:02,746] [INFO] Selected 29 target genomes.
[2024-01-25 18:05:02,746] [INFO] Target genome list was writen to GCF_030262575.1_ASM3026257v1_genomic.fna/target_genomes.txt
[2024-01-25 18:05:02,776] [INFO] Task started: fastANI
[2024-01-25 18:05:02,776] [INFO] Running command: fastANI --query /var/lib/cwl/stge3dd1090-606a-4174-ac39-dbe5dd58cbab/GCF_030262575.1_ASM3026257v1_genomic.fna.gz --refList GCF_030262575.1_ASM3026257v1_genomic.fna/target_genomes.txt --output GCF_030262575.1_ASM3026257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:07,162] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:07,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc67f4fa2-4684-4577-9716-a7f888766dda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:07,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc67f4fa2-4684-4577-9716-a7f888766dda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:07,180] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:06:07,180] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:06:07,180] [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 davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	89.7157	2170	2809	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.8227	1929	2809	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.7474	1418	2809	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	85.7148	1977	2809	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	85.7043	1993	2809	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	85.5723	1864	2809	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	85.5219	1795	2809	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.4273	1735	2809	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.3968	1673	2809	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.3285	1733	2809	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.2839	1723	2809	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.2787	1697	2809	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	85.213	1705	2809	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	85.1804	1386	2809	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	85.145	1714	2809	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	85.0935	1726	2809	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	85.0177	1704	2809	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34	GCA_000696595.1	1437453	1437453	type	True	84.9246	1467	2809	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.9147	1597	2809	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	84.9056	1520	2809	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	84.8936	1837	2809	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.8733	1424	2809	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	84.6796	1758	2809	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	84.6587	1723	2809	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	84.6514	1693	2809	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	84.6089	1683	2809	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	84.4221	1785	2809	95	below_threshold
Streptomyces malaysiense	strain=MUSC 136	GCA_000980885.2	1428626	1428626	type	True	84.1521	1516	2809	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	84.0463	1532	2809	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:07,181] [INFO] DFAST Taxonomy check result was written to GCF_030262575.1_ASM3026257v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:07,182] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:07,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:07,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc67f4fa2-4684-4577-9716-a7f888766dda/dqc_reference/checkm_data
[2024-01-25 18:06:07,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:07,260] [INFO] Task started: CheckM
[2024-01-25 18:06:07,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030262575.1_ASM3026257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030262575.1_ASM3026257v1_genomic.fna/checkm_input GCF_030262575.1_ASM3026257v1_genomic.fna/checkm_result
[2024-01-25 18:08:11,161] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:11,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:11,189] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:11,189] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:11,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030262575.1_ASM3026257v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:11,191] [INFO] Task started: Blastn
[2024-01-25 18:08:11,191] [INFO] Running command: blastn -query GCF_030262575.1_ASM3026257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc67f4fa2-4684-4577-9716-a7f888766dda/dqc_reference/reference_markers_gtdb.fasta -out GCF_030262575.1_ASM3026257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:13,322] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:13,324] [INFO] Selected 17 target genomes.
[2024-01-25 18:08:13,325] [INFO] Target genome list was writen to GCF_030262575.1_ASM3026257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:13,340] [INFO] Task started: fastANI
[2024-01-25 18:08:13,340] [INFO] Running command: fastANI --query /var/lib/cwl/stge3dd1090-606a-4174-ac39-dbe5dd58cbab/GCF_030262575.1_ASM3026257v1_genomic.fna.gz --refList GCF_030262575.1_ASM3026257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030262575.1_ASM3026257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:54,783] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:54,793] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:08:54,794] [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_900091315.1	s__Streptomyces sp900091315	99.1958	2569	2809	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_000349325.1	s__Streptomyces davaonensis	89.716	2170	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715615.1	s__Streptomyces cinnabarinus	89.3707	2186	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014257025.1	s__Streptomyces sp014257025	88.7159	2009	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	87.2928	1951	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704715.1	s__Streptomyces chartreusis	85.7034	1993	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.83	96.55	0.93	0.86	10	-
GCF_000761215.1	s__Streptomyces glaucescens	85.4805	1674	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000696115.1	s__Streptomyces olindensis	85.4424	1822	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	85.324	1718	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.2168	1856	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827025.1	s__Streptomyces sp009827025	85.2013	1710	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.69	97.69	0.89	0.89	2	-
GCF_004343515.1	s__Streptomyces sp004343515	85.1542	1824	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.56	96.56	0.86	0.86	2	-
GCF_001636945.1	s__Streptomyces sp001636945	84.8275	1654	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376565.1	s__Streptomyces hokutonensis	84.4487	1780	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.37	96.37	0.82	0.82	2	-
GCF_016654115.1	s__Streptomyces sp016654115	84.3962	1716	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.80	0.86	0.86	2	-
GCF_001417775.1	s__Streptomyces sp001417775	84.1172	1548	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317595.1	s__Streptomyces ipomoeae	83.8766	1591	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:54,795] [INFO] GTDB search result was written to GCF_030262575.1_ASM3026257v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:54,796] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:54,799] [INFO] DFAST_QC result json was written to GCF_030262575.1_ASM3026257v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:54,799] [INFO] DFAST_QC completed!
[2024-01-25 18:08:54,800] [INFO] Total running time: 0h4m19s